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PubMed1981

Risk factors for postoperative pneumonia.

Prospectively studied were 520 patients undergoing elective thoracic, upper abdominal and lower abdominal surgeries to analyze risk factors for postoperative pneumonias. Over-all, pneumonias developed in 91 of the 520 patients studied (17.5 percent). The acquisition of pneumonia was highly associated with preoperative markers of the severity of underlying diseases such as low serum albumin concentrations on admission (P less than 0.005) and high American Society of Anesthesiologists pre-anesthesia physical status classification (P less than 0.0001). History of smoking (P less than 0.001), longer preoperative stays (P less than 0.0001), longer operative procedures (P less than 0.0001) and thoracic or upper abdominal sites of surgery (P less than 0.0001) were also significant risk factors for postoperative pneumonias. Although massive obesity, old age and male sex were also associated with increased incidences of pneumonia, statistical significance was lost when these variables were controlled for site or duration of surgery. We were able to identify risk factors for pneumonia and to define a subpopulation of patients in which the risk of pneumonia was negligible. The acquisition of pneumonia by a low-risk patient should alert the physician to the possibility of a potentially preventable nosocomial infection.

Adult↗

PubMed1989

Cerebral lateralization of language in deaf and hearing people.

In Experiment 1 neither hearing nor prelingually deaf signing adolescents showed marked lateralization for lexical decision but, unlike the hearing, the deaf were not impaired by the introduction of pseudohomophones. In Experiment 2 semantic categorization produced a left hemisphere advantage in the hearing for words but not pictures whereas in the deaf words and signs but not pictures showed a right hemisphere advantage. In Experiment 3 the lexical decision and semantic categorization findings were confirmed and both groups showed a right hemisphere advantage for a face/nonface decision task. The possible effect of initial language acquisition on the development of hemispheric lateralization for language is discussed.

Adolescent↗

PubMed2004

Serial mechanisms in lexical access: the rank hypothesis.

There is general agreement that the effect of frequency on lexical access time is roughly logarithmic, although little attention has been given to the reason for this. The authors argue that models of lexical access that incorporate a frequency-ordered serial comparison or verification procedure provide an account of this effect and predict that the underlying function directly relates access time to the rank order of words in a frequency-ordered set. For both group data and individual data, it is shown that rank provides a better fit to the data than does a function based on log frequency. Extensions to a search model are proposed that account for error rates and latencies and the effect of age of acquisition, which is interpreted as an effect of cumulative frequency.

Analysis of Variance↗

PubMed2003

Pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in P. syringae pv. syringae B728a.

Pseudomonas syringae is a plant pathogen whose pathogenicity and host specificity are thought to be determined by Hop/Avr effector proteins injected into plant cells by a type III secretion system. P. syringae pv. syringae B728a, which causes brown spot of bean, is a particularly well-studied strain. The type III secretion system in P. syringae is encoded by hrp (hypersensitive response and pathogenicity) and hrc (hrp conserved) genes, which are clustered in a pathogenicity island with a tripartite structure such that the hrp/hrc genes are flanked by a conserved effector locus and an exchangeable effector locus (EEL). The EELs of P. syringae pv. syringae B728a, P. syringae strain 61, and P. syringae pv. tomato DC3000 differ in size and effector gene composition; the EEL of P. syringae pv. syringae B728a is the largest and most complex. The three putative effector proteins encoded by the P. syringae pv. syringae B728a EEL--HopPsyC, HopPsyE, and HopPsyV--were demonstrated to be secreted in an Hrp-dependent manner in culture. Heterologous expression of hopPsyC, hopPsyE, and hopPsyV in P. syringae pv. tabaci induced the hypersensitive response in tobacco leaves, demonstrating avirulence activity in a nonhost plant. Deletion of the P. syringae pv. syringae B728a EEL strongly reduced virulence in host bean leaves. EELs from nine additional strains representing nine P. syringae pathovars were isolated and sequenced. Homologs of avrPphE (e.g., hopPsyE) and hopPsyA were particularly common. Comparative analyses of these effector genes and hrpK (which flanks the EEL) suggest that the EEL effector genes were acquired by horizontal transfer after the acquisition of the hrp/hrc gene cluster but before the divergence of modern pathovars and that some EELs underwent transpositions yielding effector exchanges or point mutations producing effector pseudogenes after their acquisition.

Bacterial Proteins↗

PubMed2002

Neural correlates for the acquisition of natural language syntax.

Some types of simple and logically possible syntactic rule never occur in human language grammars, leading to a distinction between grammatical and nongrammatical syntactic rules. Comparison of the neuroanatomical correlates underlying the acquisition of grammatical and nongrammatical rules can provide relevant evidence on the neural processes dedicated to language acquisition in a given developmental stage. Until present no direct evidence on the neural mechanisms subserving language acquisition at any developmental stage has been supplied. We used fMRI in investigating the acquisition of grammatical and nongrammatical rules in the specified sense in 14 healthy adults. Grammatical rules compared with nongrammatical rules specifically activated a left hemispheric network including Broca's area, as shown by direct comparisons between the two rule types. The selective role of Broca's area was further confirmed by time x condition interactions and by proficiency effects, in that higher proficiency in grammatical rule usage, but not in usage of nongrammatical rules, led to higher levels of activation in this area. These findings provide evidence for the neural mechanisms underlying language acquisition in adults.

Adult↗

PubMed1994

Rodent L1 evolution has been driven by a single dominant lineage that has repeatedly acquired new transcriptional regulatory sequences.

All mammalian genomes contain approximately 100,000 copies of the transposable element LINES-1 (L1). Phylogenetic analysis indicates that the L1 progenitor predates the mammalian radiation; since that time, the open reading frames encoded in L1 have evolved under selection. The least conserved regions within L1 are the 5'-terminal transcriptional regulatory sequences. In rodents, four types of L1 elements (A, F, and V from mouse and R from rat) have been defined according to the type of apparently nonhomologous promoter sequence present at the 5' end. In this study, we investigate the relationships between these four types of promoters. DNA sequence was determined from approximately 1.5-kb regions from the 5' ends of seven F- and three V-type L1 elements. These sequences were aligned with 29 previously reported L1 elements. Phylogenetic analysis was then performed on the homologous regions of the alignment. The results indicate that in mouse all of the A-, F-, and V-type elements belong to a single dominant lineage but were inserted into the genome during different time periods; V-type elements are the oldest, while A-type elements are the most recently inserted. V-type elements also appear ancestral to the R-type elements found in rat and therefore were replicatively competent prior to the divergence of rat and mouse. Analysis of sequence identity indicates that the different 5' promoters did not derive from a common ancestor. Therefore, the dominant L1 lineage appears to have acquired novel promoter sequences from non-L1 sources. Transposable elements from a wide range of species show similar structural rearrangements, suggesting that acquisition of new sequences may be a common theme in their evolution.

Animals↗

PubMed1996

Ethnic networks and language proficiency among immigrants.

"This paper uses a unique data set for Australia (1988) that includes a variety of ethnic network variables to analyze the role of the language concentration measure [in immigrants' acquisition of the language of the destination country]. These ethnic variables, in particular, ethnic press, relatives in Australia, and spouse's origin language, are highly statistically significant. Their inclusion in the equation eliminates the effect of the minority-language concentration variable. The model for analyzing the determinants of English reading and English writing skills in Australia is also shown to be very similar to the model for speaking fluency, including the effect of the ethnic network variables."

Acculturation↗

PubMed2004

Ancestral gene fusion in cellobiose dehydrogenases reflects a specific evolution of GMC oxidoreductases in fungi.

Cellobiose dehydrogenases (CDHs) are extracellular hemoflavoenzymes that are thought to be involved in the degradation of two of the most abundant biopolymers in the biosphere, cellulose and lignin. To date, these enzymes, consisting of a cytochrome domain and a flavin domain, have been detected and sequenced exclusively in the kingdom of fungi. Independent phylogenetic analyses of two distinct domains of CDH genes reveal that they evolved in parallel as fused genes. Whereas the cytochrome domains are unique sequence motifs, the flavin domains clearly belong to the glucose-methanol-choline (GMC) oxidoreductase family--an evolution line of widespread flavoproteins extending from the Archae to higher eukaryotes. The most probable unrooted phylogenetic tree obtained from our analysis of 52 selected GMC members reveals five principal evolutionary branches: cellobiose dehydrogenase, cholesterol oxidase (COX), hydroxynitrile lyase, alcohol oxidase (AOX)/glucose oxidase (GOX)/choline dehydrogenase, and a branch of dehydrogenases with various specificities containing also an Archaeon open reading frame (ORF). Cellobiose dehydrogenases cluster with cholesterol oxidases and the clade of various specificities, whereas hydroxynitrile lyases are closely related to glucose oxidases, alcohol oxidases, and choline dehydrogenases. The results indicate that the evolutionary line from a primordial GMC flavoprotein to extant cellobiose dehydrogenases was augmented after an early acquisition of the cytochrome domain to form two distinct branches for basidiomycetes and ascomycetes. One ascomycetous evolutionary line of CDHs has acquired a carbohydrate-binding module (CBM) of type 1, the sequence of which is similar to that of corresponding domains in several glycosidases. This is the first attempt towards a comprehensive phylogenetic analysis of cellobiose dehydrogenases.

Alcohol Oxidoreductases↗

PubMed1999

The kindergarten-path effect: studying on-line sentence processing in young children.

A great deal of psycholinguistic research has focused on the question of how adults interpret language in real time. This work has revealed a complex and interactive language processing system capable of rapidly coordinating linguistic properties of the message with information from the context or situation (e.g. Altmann & Steedman, 1988; Britt, 1994; Tanenhaus, Spivey-Knowlton, Eberhard & Sedivy, 1995; Trueswell & Tanenhaus, 1991). In the study of language acquisition, however, surprisingly little is known about how children process language in real time and whether they coordinate multiple sources of information during interpretation. The lack of child research is due in part to the fact that most existing techniques for studying language processing have relied upon the skill of reading, an ability that young children do not have or are only beginning to acquire. We present here results from a new method for studying children's moment-by-moment language processing abilities, in which a head-mounted eye-tracking system was used to monitor eye movements as participants responded to spoken instructions. The results revealed systematic differences in how children and adults process spoken language: Five Year Olds did not take into account relevant discourse/pragmatic principles when resolving temporary syntactic ambiguities, and showed little or no ability to revise initial parsing commitments. Adults showed sensitivity to these discourse constraints at the earliest possible stages of processing, and were capable of revising incorrect parsing commitments. Implications for current models of sentence processing are discussed.

Adult↗

PubMed1999

The mithramycin gene cluster of Streptomyces argillaceus contains a positive regulatory gene and two repeated DNA sequences that are located at both ends of the cluster.

Sequencing of a 4.3-kb DNA region from the chromosome of Streptomyces argillaceus, a mithramycin producer, revealed the presence of two open reading frames (ORFs). The first one (orfA) codes for a protein that resembles several transport proteins. The second one (mtmR) codes for a protein similar to positive regulators involved in antibiotic biosynthesis (DnrI, SnoA, ActII-orf4, CcaR, and RedD) belonging to the Streptomyces antibiotic regulatory protein (SARP) family. Both ORFs are separated by a 1.9-kb, apparently noncoding region. Replacement of the mtmR region by an antibiotic resistance cassette completely abolished mithramycin biosynthesis. Expression of mtmR in a high-copy-number vector in S. argillaceus caused a 16-fold increase in mithramycin production. The mtmR gene restored actinorhodin production in Streptomyces coelicolor JF1 mutant, in which the actinorhodin-specific activator ActII-orf4 is inactive, and also stimulated actinorhodin production by Streptomyces lividans TK21. A 241-bp region located 1.9 kb upstream of mtmR was found to be repeated approximately 50 kb downstream of mtmR at the other end of the mithramycin gene cluster. A model to explain a possible route for the acquisition of the mithramycin gene cluster by S. argillaceus is proposed.

Amino Acid Sequence↗

PubMed1998

Yellow fever 5' noncoding region as a potential element to improve hepatitis C virus production through modification of translational control.

The lengthy 5' noncoding region (5' NCR) of hepatitis C virus (HCV) RNA forms a highly ordered secondary structure, very conserved among different strains. It includes an internal ribosome entry site (IRES) element, responsible for the cap-independent translation initiation of HCV RNA. Similarly to the IRES of hepatitis A virus (HAV), another human hepatitis virus, HCV IRES, activity in internal initiation of translation is weak. Furthermore, both viruses exhibit a poor growth phenotype that may result at least partially from an inhibitory control of translation. To enhance HCV translation, as a preliminary step in designing constructs for improvement in viral production, we sought to evaluate a chimeric construct containing the yellow fever virus (YFV) 5' NCR fused to the initiation codon of the HCV coding sequence. YF viral RNA, as the majority of eukaryotic messenger RNAs, is translated by a ribosome scanning mechanism in a cap-dependent manner. The efficiency of translation initiation of the parental HCV construct was compared in vitro in rabbit reticulocyte lysates with that of the chimeric construct containing YFV 5' NCR. Surprisingly, the related distanced YFV 5' NCR was fivefold more active than was the wild-type HCV IRES in directing that function. Furthermore, chimeric transcripts were shown to be effective in vivo after transfection of eukaryotic cells. Taken together, these results raise the following question: why has the HCV genus evolved to the acquisition of an IRES element within its 5' NCR among the Flaviviridae family?

5' Untranslated Regions↗

PubMed1996

Flow cytometry for CD34 determination in hematopoietic grafts.

CD34 is a type I transmembrane protein that is expressed on lympho-hematopoietic progenitor and endothelial cells and has a potential adhesion function. Various monoclonal antibodies, whether characterized by glycosylated epitopes or not, are utilized to recognize different subsets of hematopoietic progenitors. Coexpression of membrane markers involving CD34 is an approach to the definition of those subpopulations of cells previously characterized by using in vitro cultures. Thus, in the autologous transplantation procedure, flow cytometry determination of CD34+ cells in the grafts themselves, especially as concerns cytapheresis products, was enhanced with CFU-GM enumeration. This methodology required a standardized protocol with regard to the choice of the monoclonal antibody, had to be to data acquisition and to computer analysis. Within the framework of a multicentric trial, various strategies had to be evaluated. Special attention was paid to obtaining a sensitivity level of 0.1%. New, standardized approaches are currently in the planning stage, in particular with a view to determining absolute count on the basis of readings generated by the flow-cytometer.

Antigens, CD34↗

PubMed1996

Impairments of number processing induced by prenatal alcohol exposure.

Prenatal alcohol exposure causes a variety of cognitive deficits, notably in mathematics and higher order processes such as abstraction. An exploratory battery was developed to examine specific types of number processing impairments in 29 adolescent and adult patients with Fetal Alcohol Syndrome (FAS) and Fetal Alcohol Effects (FAE) relative to controls matched for age, gender, and educational level. The battery included 11 tests: number reading and writing, exact calculation (addition, multiplication, subtraction), approximate calculation (selecting a plausible result for an operation), number comparison, proximity judgment, and cognitive estimation. The results indicated particular difficulties in calculation and estimation tests, with intact number reading and writing ability. The greatest impairment was found in the cognitive estimation test, which is sensitive to frontal lobe lesions. The patterns of deficit described may reflect either the diffuseness of brain damage incurred from prenatal alcohol exposure, or a cumulative deficit in comprehension which may be important for the acquisition of higher-order mathematical abilities.

Adolescent↗

PubMed1997

Vertebral morphometry studies using dual-energy x-ray absorptiometry.

Vertebral fractures are one of the most common consequences of osteoporosis. They are usually diagnosed by visual interpretation of lateral radiographs of the lumbar and thoracic spine. Vertebral morphometry, based on measurements of the anterior, middle, and posterior heights of the vertebral bodies from T4 to L4, is a useful adjunct to the visual reading of radiographs. A new generation of dual-energy x-ray absorptiometry (DXA) scanners offers software for acquiring lateral images of the spine and performing vertebral morphometry analysis. Advantages of DXA morphometry include straightforward and reproducible patient positioning, absence of geometrical distortion of the image, low radiation dose, digital acquisition, and simplified, semi-automated scan analysis. The widespread availability of such DXA systems should make the investigation of vertebral fractures more widely accessible.

Absorptiometry, Photon↗

PubMed1998

A distinctive class of integron in the Vibrio cholerae genome.

The ability of bacteria to acquire and disseminate heterologous genes has been a major factor in the development of multiple drug resistance. A gene, intI4, was identified that encodes a previously unknown integrase that is associated with a "gene-VCR" organization (VCRs are Vibrio cholerae repeated sequences), similar to that of the well-characterized antibiotic resistance integrons. The similarity was confirmed by IntI1-mediated recombination of a gene-VCR cassette into a class 1 integron. VCR cassettes are found in a number of Vibrio species including a strain of V. metschnikovii isolated in 1888, suggesting that this mechanism of heterologous gene acquisition predated the antibiotic era.

Amino Acid Sequence↗

PubMed1996

Molecular characterization of a heme-binding protein of Bacteroides fragilis BE1.

An iron-repressible 44-kDa outer membrane protein plays a crucial role in the acquisition of heme by the anaerobic bacterium Bacteroides fragilis. The DNA sequence of the gene encoding the 44-kDa protein (hupA) was determined. The hupA gene encodes a protein of 431 amino acid residues with a calculated molecular mass of 48,189 Da. The hupA gene is preceded by an open reading frame of 480 bp that probably encodes a protein with a calculated molecular mass of 18,073 Da. hupA and this open reading frame are likely organized in an operon, and a sequence homologous to the Escherichia coli consensus Fur box was present in the putative promoter region of the operon. Heme-binding studies showed that HupA binds heme. Analysis of the deduced amino acid sequence revealed signature heme-binding consensus motifs, characteristic of heme lyases. Subcellular localization studies in E. coli revealed that HupA was mainly found in the cytoplasmic membrane but not in the outer membrane of E. coli. This suggested that B. fragilis uses another strategy for the translocation of this outer membrane protein across its cell envelope than E. coli does. HupA did not have significant homology with other putative bacterial heme receptors.

Amino Acid Sequence↗

PubMedDate not supplied

A new approach to RIS/DR interconnection.

The article focuses on a new, standards-based approach for linking modalities to a radiology information system (RIS) in the radiology department. Computers have been used in radiology for quite some time-for the complex processing of algorithms used by CT and MR, for example. The advent of computed radiography (CR) and direct radiography (DR) has helped bring x-ray film into the world of computers. DR uses a technology similar to that in digital cameras to convert the intensity and location of the diagnostic image into digital form. Many radiology departments now store images on disks and read from computer monitors in a reading room. With its high-volume radiology department, the Cleveland Clinic Foundation (CCF) has been a long-time user of one particular RIS system. As the department moved to DR implementation, it required a means to automatically include patient demographic information with the image at the time of study acquisition, so this information would be associated with the image throughout its history. Using an approach developed by several companies in connection with CCF, technologists now use only two interfaces on one computer screen. Further, a technologist can close the study from the DR unit, allowing more time for patient care. The collaborative effort between CCF and the companies involved has resulted in an exciting standards-based approach to linking its RIS and DR systems.

Data Display↗

PubMed2001

New simulators for the optimum management and operation of wastewater treatment plant.

This paper presents the basic description and the first full-scale implementation of a new kind of simulator specially designed to facilitate and improve the management and operation of modern wastewater treatment plants (WWTP). This new kind of simulator for plant operation is specifically adapted to every WWTP and the software is developed considering the common needs of the operators in plant exploitation. The internal structure of the plant operation simulator is based on a complete connection between the real data and the mathematical model of the plant. The software is then able to perform the processing, storage and management of the plant data and to predict the evolution of the process reading the required inputs from its stored files. The results obtained with the first application recommend the implementation of this new kind of simulators for plant operation in other treatment plants. However, it is important to note that the application of this technology implies a systematic and rigorous methodology in the acquisition and processing of the most significant plant data.

Data Collection↗