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51.
MOTIVATION: Searching a protein sequence database for homologs is a
powerful tool for discovering the structure and function of a sequence. Two
new methods for searching sequence databases have recently been described:
Probabilistic Smith-Waterman (PSW), which is based on Hidden Markov models
for a single sequence using a standard scoring matrix, and a new version of
BLAST (WU-BLAST2), which uses Sum statistics for gapped alignments.
RESULTS: This paper compares and contrasts the effectiveness of these
methods with three older methods (Smith- Waterman: SSEARCH, FASTA and
BLASTP). The analysis indicates that the new methods are useful, and often
offer improved accuracy. These tools are compared using a curated (by Bill
Pearson) version of the annotated portion of PIR 39. Three different
statistical criteria are utilized: equivalence number, minimum errors and
the receiver operating characteristic. For complete-length protein query
sequences from large families, PSW's accuracy is superior to that of the
other methods, but its accuracy is poor when used with partial-length query
sequences. False negatives are twice as common as false positives
irrespective of the search methods if a family-specific threshold score
that minimizes the total number of errors (i.e. the most favorable
threshold score possible) is used. Thus, sensitivity, not selectivity, is
the major problem. Among the analyzed methods using default parameters, the
best accuracy was obtained from SSEARCH and PSW for complete-length
proteins, and the two BLAST programs, plus SSEARCH, for partial-length
proteins.
相似文献
52.
Trevor R. Gulbrandsen Mary Kate Skalitzky Sarah E. Ryan Burke Gao Alan G. Shamrock Timothy S. Brown Jacob M. Elkins 《The Iowa orthopaedic journal》2022,42(2):98
BackgroundPatients often turn to the online resources to learn about orthopedic procedures. As the rate of joint arthroplasty is projected to increase, the corresponding interest in relevant online education material will increase as well. The American Medical Association (AMA) and National Institutes of Health (NIH) recommend that publicly available online health information be written at the 6th grade or lower reading level to be fully understood by the average adult in the United States. Additionally, educational resources should be written such that readers can process key information (understandability) or identify available actions to take (actionability). The purpose of this study was to quantify the readability, understandability, and actionability of online patient educational materials regarding total knee arthroplasty (TKA).MethodsThe most common Google™ search term utilized by the American public was determined to be “knee replacement”. Subsequently two independent online searches (Google.com) were performed. From the top 50 search results, websites were included if directed at educating patients regarding TKA. Non-text websites (audiovisual), articles (news/research/industry), and unrelated resources were excluded. Readability was quantified using the following valid objective algorithms: Flesch-Kincaid Grade-Level (FKGL), Simple Measure of Gobbledygook (SMOG) grade, Coleman-Liau Index (CLI), and Gunning-Fog Index (GFI). PEMAT was utilized to assess understandability and actionability (0-100%; score ≥70% indicates acceptable scoring). The relationship between search rank with FKGL and PEMAT scores was quantified.ResultsA total of 34 (68%) unique websites met inclusion criteria. The mean FKGL, SMOG, CLI, and GFI was 11.8±1.6, 11.1±1.2, 11.9±1.4, and 14.7±1.6, respectively. None of the websites scored within the acceptable NIH/AMA recommended reading levels. Mean understandability and actionability scores were 54.9±12.1 and 30.3±22.0. Only 5.9% (n=2) and 9.2% (n=1) of websites met the ≥70% threshold for understandability and actionability. Only 29.4% (n=10) sources used common language and only 26.9% (n=9) properly defined complicated medical terms. Based on website type, the mean understandability scores for academic institution, private practice, and health information publisher websites were 57.2±8.8%, 52.6±11.1%, and 54.3±15.3% (p=0.67). Readability (rho: -0.07; p=0.69), understandability (rho: -0.02; p=0.93), and actionability (rho: -0.22; p=0.23) scores were not associated with Google™ search rank.ConclusionTKA materials scored poorly with respect to readability, understandability, and actionability. None of the resources scored within the recommended AMA/NIH reading levels. Only 5.9% scored adequately on understandability measures. Substantial efforts are needed to improve online resources to optimize patient comprehension and facilitate informed decision-making. Level of Evidence: III 相似文献
53.
Recent horizontal transfer of a mariner transposable element among and between Diptera and Neuroptera 总被引:11,自引:4,他引:7
Transposable elements of the mariner family are widespread among insects
and other invertebrates, and initial analyses of their relationships
indicated frequent occurrence of horizontal transfers between hosts. A
specific PCR assay was used to screen for additional members of the
irritans subfamily of mariners in more than 400 arthropod species.
Phylogenetic analysis of cloned PCR fragments indicated that relatively
recent horizontal transfers had occurred into the lineages of a fruit fly
Drosophila ananassae, the horn fly Haematobia irritans, the African malaria
vector mosquito Anopheles gambiae, and a green lacewing Chrysoperla
plorabunda. Genomic dot-blot analysis revealed that the copy number in
these species varies widely, from about 17,000 copies in the horn fly to
three copies in D. ananassae. Multiple copies were sequenced from genomic
clones from each of these species and four others with related elements.
These sequences confirmed the PCR results, revealing extremely similar
elements in each of these four species (greater than 88% DNA and 95% amino
acid identity). In particular, the consensus sequence of the transposase
gene of the horn fly elements differs by just two base pairs out of 1,044
from that of the lacewing elements. The mosquito lineage has diverged from
the other Diptera for over 200 Myr, and the neuropteran last shared a
common ancestor with them more than 265 Myr ago, so this high similarity
implies that these transposons recently transferred horizontally into each
lineage. Their presence in only the closest relatives in at least the
lacewing lineage supports this hypothesis. Such horizontal transfers
provide an explanation for the evolutionary persistence and widespread
distribution of mariner transposons. We propose that the ability to
transfer horizontally to new hosts before extinction by mutation in the
current host constitutes the primary selective constraint maintaining the
sequence conservation of mariners and perhaps other DNA-mediated elements.
相似文献
54.
The effects of 18-crown-6 on the synthesis of peptides catalyzed by alpha-chymotrypsin are reported. Lyophilization of the enzyme in the presence of 50 equivalents of 18-crown-6 results in a 425-fold enhanced activity when the reaction between the 2-chloroethylester of N-acetyl-L-phenylalanine and L-phenylalaninamide is carried out in acetonitrile. Addition of crown ether renders the dipeptide synthesis in nonaqueous solvents catalyzed by alpha-chymotrypsin possible on a preparative scale. The acceleration is observed in different solvents and for various peptide precursors. Copyright 1998 John Wiley & Sons, Inc. 相似文献
55.
P S Dragovich R Zhou D J Skalitzky S A Fuhrman A K Patick C E Ford J W Meador S T Worland 《Bioorganic & medicinal chemistry》1999,7(4):589-598
The optimization of a series of irreversible human rhinovirus (HRV) 3C protease (3CP) inhibitors is described. These inhibitors are comprised of an L-Leu-L-Phe-L-Gln tripeptide containing an N-terminal amide moiety and a C-terminal ethyl propenoate Michael acceptor. Examination of approximately 500 compounds with varying N-terminal amides utilizing solid-phase synthesis and high-throughput assay techniques is described along with the solution phase preparation of several highly active molecules. A tripeptide Michael acceptor containing an N-terminal amide derived from 5-methylisoxazole-3-carboxylic acid is shown to exhibit potent, irreversible anti-3CP activity (k(obs)/[I] = 260,000 M(-1) s(-1); type-14 3CP) and broad-spectrum antirhinoviral properties (average EC50 = 0.47 microM against four different HRV serotypes). 相似文献
56.
Motomi Ito Kuniaki Watanabe Yoko Kita Takayuki Kawahara DJ Crawford Tetsukazu Yahara 《Journal of plant research》2000,113(1):79-89
Eupatorium were examined by sequencing the internal transcribed spacers (ITS) of nuclear ribosomal DNA and restriction site analysis
of chloroplast DNA. Molecular data provided strong evidence that (1) this genus originated in North America, (2) the genus
diverged into three morphological species groups, Eutrochium, Traganthes and Uncasia in North America, and (3) one of the North American Uncasia lineages migrated into temperate Europe and eastern Asia over the Bering land bridge. The estimated divergence times support
a late Miocene to early Pliocene migration from North America to Eurasia via the Bering land bridge. A European species was
sister to all of the eastern Asian species examined. The disjunct distribution pattern of the genus Eupatorium is incongruent with the classical Arcto-Tertiary geoflora concept.
Received 13 September 1999/ Accepted in revised form 4 January 2000 相似文献
57.
The effects of selective ibotenate lesions of the complete hippocampus (CHip), the hippocampal ventral pole (VP), or the medial prefrontal cortex (mPFC) in male rats were assessed on several measures related to energy regulation (i.e., body weight gain, food intake, body adiposity, metabolic activity, general behavioral activity, conditioned appetitive responding). The testing conditions were designed to minimize the nonspecific debilitating effects of these surgeries on intake and body weight. Rats with CHip and VP lesions exhibited significantly greater weight gain and food intake compared with controls. Furthermore, CHip-lesioned rats, but not rats with VP lesions, showed elevated metabolic activity, general activity in the dark phase of the light-dark cycle, and greater conditioned appetitive behavior, compared with control rats without these brain lesions. In contrast, rats with mPFC lesions were not different from controls on any of these measures. These results indicate that hippocampal damage interferes with energy and body weight regulation, perhaps by disrupting higher-order learning and memory processes that contribute to the control of appetitive and consummatory behavior. 相似文献
58.
59.
We report here the structural determination of N-linked oligosaccharides
found on extracellular hemoglobins of the hydrothermal vent tube worm
Riftia pachyptila. Structures were elucidated by a combination of
electrospray ionization tandem mass spectrometry, matrix- assisted laser
desorption/ionization mass spectrometry, normal-phase high performance
liquid chromatography, and exoglycosidase digestion. The sugar chains were
found to consist mainly of high-mannose-type glycans with some structures
partially capped by one or two terminal glucose residues. The present study
represents the first report of the occurrence of glucose capping of
N-linked carbohydrates in a secreted glycoprotein of a metazoan.
Previously, glucose capping has only been described for a membrane-bound
surface glycoprotein from the unicellular parasite Leishmania mexicana
amazonensis.
相似文献
60.
In limulus sperm an actin filament bundle 55 mum in length extends from the acrosomal vacuole membrane through a canal in the nucleus and then coils in a regular fashion around the base of the nucleus. The bundle expands systematically from 15 filaments near the acrosomal vacuole to 85 filaments at the basal end. Thin sections of sperm fixed during stages in spermatid maturation reveal that the filament bundle begins to assemble on dense material attached to the acrosomal vacuole membrane. In micrographs fo these early stages in maturation, short bundles are seen extending posteriorly from the dense material. The significance is that these short, developing bundles have about 85 filaments, suggesting that the 85-filament end of the bundle is assembled first. By using filament bundles isolated and incubated in vitro with G actin from muscle, we can determine the end “preferred” for addition of actin monomers during polymerization. The end that would be associated with the acrosomal vacuole membrane, a membrane destined to be continuous with the plasma membrane, is preferred about 10 times over the other, thicker end. Decoration of the newly polymerized portions of the filament bundle with subfragment 1 of myosin reveals that the arrowheads point away from the acrosomal vacuole membrane, as is true of other actin filament bundles attached to membranes. From these observations we conclude that the bundle is nucleated from the dense material associated with the acrosomal vacuole and that monomers are added to the membrane-associated end. As monomers are added at the dense material, the thick first-made end of the filament bundle is pushed down through the nucleus where, upon reaching the base of the nucleus, it coils up. Tapering is brought about by the capping of the peripheral filaments in the bundle. 相似文献