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Biomedical subjects

L M Hsu

Publications and source records attributed to L M Hsu.

18 recordsLinked to original sources

Effects of directionality of significance tests on the bias of accessible effect sizes.

The proportion of studies that use one-tailed statistical significance tests (pi) in a population of studies targeted by a meta-analysis can affect the bias of the sample effect sizes (sample ESs, or ds) that are accessible to the meta-analyst. H. C. Kraemer, C. Gardner, J. O. Brooks, and J. A. Yesavage (1998) found that, assuming pi = 1.0, for small studies (small Ns) the overestimation bias was large for small population ESs (delta < or = 0.2) and reached a maximum for the smallest population ES (viz., delta = 0). The present article shows (with a minor modification of H. C. Kraemer et al.'s model) that when pi = 0, the small-N bias of accessible sample ESs is relatively small for delta < or = 0.2, and a minimum (in fact, nonexistent) for delta = 0. Implications are discussed for interpretations of meta-analyses of (a) therapy efficacy and therapy effectiveness studies, (b) comparative outcome studies, and (c) studies targeting small but important population ESs.

Bias↗

Analysis of saponins from black bean by electrospray ionization and fast atom bombardment tandem mass spectrometry.

Saponins from black bean (Vigna mungo L. Hepper) were analyzed using positive and negative ion fast atom bombardment mass spectrometry (FAB-MS) and liquid chromatography/mass spectrometry. Methanol was used to extract the saponins from defatted black bean, which was partially purified by extraction with n-butanol, and the extract was dialyzed with 3000 M(r) cut-off tubing. The dialyzate was analyzed using mass spectrometry. According to FAB-MS/MS, mixtures from black bean contain soyasaponin I as the predominant saponin. In addition, MS/MS analysis was performed in which the structures of saponins of black bean cotyledon were determined to be soyasaponin I, soyasaponin II, soyasaponin V, 3-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-galactopyranosyl-(1 --> 2)-beta-D-glucuronopyranosyl]complogenin (saponin A) and 3-O-[alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosyl-(1 --> 2)-beta-D-glucopyranosyl]oleanolic acid (saponin B). For the black bean shell and the root of black bean sprout, analysis confirmed the saponins of soyasaponin I, soyasaponin II, soyasaponin V, saponin A, saponin B, acetylsoyasaponin A(4) and soyasaponin beta(g). Moreover, all the studied saponins were found in the stem and leaves of the black bean sprouts, except soyasaponin beta(g) and acetylsoyasaponin A(4), respectively.

Carbohydrate Sequence↗

A comparison of three methods of identifying reliable and clinically significant client changes: commentary on Hageman and Arrindell.

Objectives of this commentary are to (1) note major similarities and differences of three methods of identifying reliable and clinically significant client changes, (2) demonstrate how graphs can be used to identify reliable and clinically significant client changes with each method, (3) describe uses and interpretations of overlaid graphs, (4) draw attention to an alternative to the Hageman and Arrindell method of estimating true score changes, and (5) caution users of the three methods against interpreting reliable and/or clinically significant changes which occur in psychotherapy as evidence of therapy 'efficacy' or 'effectiveness'.

Data Interpretation, Statistical↗

Caveats concerning comparisons of change rates obtained with five methods of identifying significant client changes: comment on Speer and Greenbaum (1995).

Various methods have been proposed to identify clients who have improved, have not changed, or have deteriorated in psychotherapy. D. D. Speer and P. E. Greenbaum (1995) compared empirically determined change rates (proportions of clients identified as improved, unchanged, or deteriorated) obtained with 5 of these methods, tested the hypothesis that 1 method would be more sensitive than the other 4 in detecting significant changes, and recommended 2 of the 5 methods. This comment draws attention to problems related to the meaning of their comparisons of change rates and to some implications of their recommendations. These problems include misinterpretation of formulas; use of methods with questionable standard errors; confounding of effects of methods with effects of norms, data sets, and risks of misclassifying patients who do not change; absence of valid external criteria of client changes; and excessive reliance on the Jacobson-Truax method for evaluation of 2-wave data.

Humans↗

Conserved region 3 of Escherichia coli final sigma70 is implicated in the process of abortive transcription.

Multiple-round in vitro transcription assays were performed using purified Escherichia coli RNA polymerase reconstituted with either wild-type or mutant final sigma70 proteins. These mutants, final sigma70(P504L) and final sigma70(S506F), bear single amino acid changes in conserved protein region 3. Behavior of the mutant enzymes on three test templates, bearing either the T7 A1, T5 N25, or T5 N25antiDSR promoter, were characterized. Transcription of all three promoter templates produced a pattern of specific abortive RNA species, which was qualitatively different for the mutants compared to the wild-type final sigma70 enzyme. Short abortive RNAs were produced at similar levels for mutant and wild-type enzymes. The production of longer abortive species was either reduced or increased by the mutant enzymes in a systematic manner that appears promoter-specific, and could be RNA length- or promoter distance-dependent. The process of abortive RNA transcription is thought to be tightly associated with that of promoter clearance. However, promoter clearance from these templates appears only slightly affected by the mutant enzymes. These mutants implicated region 3 of final sigma70 in the process of abortive transcription and suggest that the sequence of enzymatic events leading to the production of abortive or full-length RNA may be separable.

Bacterial Proteins↗

Escherichia coli transcript cleavage factors GreA and GreB stimulate promoter escape and gene expression in vivo and in vitro.

The process of RNA chain initiation by RNA polymerases plays a central role in the regulation of transcription. In this complex phase of transcription, short oligomers are synthesized and released from the enzyme-promoter complex in a reaction termed abortive initiation. The polymerase undergoes many cycles of abortive initiation prior to completion of the initiation process, which is signaled by the translocation of the enzyme away from the promoter, release of sigma factor, and formation of an elongation complex in which the RNA is stably bound. We have studied the parameters that affect escape from the promoter by Escherichia coli RNA polymerase for the phage T7 A1 promoter, the phage T5 N25 promoter, and the chimeric promoter T5 N25antiDSR. The latter site contains a synthetic initial transcribed region that reduces its ability to synthesize RNA both in vivo and in vitro. Clearance from T5 N25antiDSR can be stimulated up to 10-fold in vitro by addition of the E. coli transcript cleavage factor GreA or GreB, but these factors have little effect on transcription from the normal T7 A1 or T5 N25 promoters. Using an E. coli strain lacking GreA and GreB, we were also able to show stimulation of transcription by the Gre factors from the T5 N25antiDSR promotor in vivo. The stimulation of RNA chain initiation by Gre factors, together with their known biochemical properties in the transcription elongation reaction, suggests some specific models for steps in the transcription initiation reaction.

Base Sequence↗

Regression toward the mean associated with measurement error and the identification of improvement and deterioration in psychotherapy.

Several factors can cause posttherapy scores to regress (relative to pretherapy scores) toward a group mean. This article focuses on regression effects that are due to measurement error, and on methods used to evaluate pre- to posttherapy score changes that attempt to take these regression effects into account. Statistical and practical problems associated with these methods are discussed. In particular, a statistical problem is identified in the most recent article that advocates use of these methods. Consequences of ignoring this problem and a way of correcting it are presented. Five practical problems encountered in using a correct classical true-score theory method of identifying reliable changes (based on derivations of H. Gulliksen [1950] and F. M. Lord and M. R. Novick [1968]) are then presented. Finally, objectives of these methods are distinguished from objectives of other strategies used to evaluate changes in psychotherapy.

Humans↗

Upstream sequence activation of Escherichia coli argT promoter in vivo and in vitro.

Escherichia coli argT promoter in a galK fusion construct is shown by BAL 31 deletion to require its upstream region for high in vivo activity. The extent of activation conferred by the upstream sequence from -130 to -38 is 25-fold. A spontaneous mutant containing a T to G transversion at -37 (i.e., the T-37G promoter) shows a similar requirement; however, the upstream sequence producing a 10-fold effect spans only -130 to -60. The difference in upstream sequence boundaries between the wild-type and T-37G promoters suggests the possible existence of two activating elements. Gel mobility investigation points to the presence of bent DNA in the argT promoter, and the bent center was localized to the -90 to -95 region by circular permutation analysis. The role of the upstream activating sequence (UAS) in promoter function was probed by competitive transcription experiments in vitro. Results of this type of analysis indicate that the full UAS activates transcription through a combined effect on KB and k2. Of these, KB is significantly strengthened by the proximal element, and k2 is stimulated to a smaller extent by the distal element. The evidence from deletion analysis, gel mobility investigation, and competitive transcription together support a "two-element" model of UAS function for the argT promoter.

Base Sequence↗

Random sampling, randomization, and equivalence of contrasted groups in psychotherapy outcome research.

Random sampling and random assignment (randomization) are some of the most popular methods of equating contrasted groups on pre-existing nuisance variables. However, the small samples typically used in psychotherapy outcome studies raise some questions about the extent to which these methods eliminate the pretreatment nonequivalence of groups in this area of research. This article identifies conditions under which equivalence is likely (and unlikely) to be attained with simple random sampling and randomization in psychotherapy efficacy studies of the kind examined in recent meta-analyses. Some consequences of nonequivalence are viewed as manifestations of Simpson's paradox. Misinterpretations of estimates of the relative efficacy of treatments are expected in view of belief in the law of small numbers. The minimum sample sizes needed to protect against nonequivalence are compared with those needed to satisfy several other criteria.

Clinical Trials as Topic↗

A comparison of HPLC and TLC in the assessment of amniotic fluid lecithin/sphingomyelin ratio.

One hundred amniotic fluid (AF) specimens of women at 28 to 37 weeks gestation were obtained during labor for lecithin/sphingomyelin ratio (L/S ratio) study by using high performance liquid chromatography (HPLC) and thin layer chromatography (TLC). The results are divided into two groups: one with L/S ratio at or more than 2, and the other with L/S ratio of less than 2. Of the 80 measured by HPLC with the ratio of above 2 or 1.3%, one suffered respiratory distress syndrome (RDS); of the 65 measured by TLC also with the ratio of above 2 or 3.1%, two developed RDS. The result bears no great significance here. However, in the groups with L/S ratio of less than two, the results were very significant: 17 of 20 estimated by HPLC happened to have RDS for an incidence of false positive rate of 15% compared with a 54.3% in 16 of the 35 women evaluated by TLC.

Amniotic Fluid↗

Escherichia coli 6S RNA gene is part of a dual-function transcription unit.

The gene coding for the metabolically stable 6S RNA of Escherichia coli has been cloned, sequenced, and partially characterized in expression analyses. The DNA sequence results confirm the accuracy of the previously established RNA sequence and, with genomic hybridization data, reveal that there is only one copy of the 6S DNA in the chromosome. Consistent with its relaxed mode of expression, the promoter region of the 6S RNA gene was found to lack the hypothetical GC-rich discriminator domain common to other stable RNA genes under stringent control. The sequence results also revealed the occurrence of a 540-base-pair open reading frame immediately downstream from the 6S RNA coding region. Results from the expression analyses show that the protein and RNA coding regions are cotranscribed in vitro and that the open reading frame is translated in vivo.

Base Sequence↗

Efficiency of local versus standard MMPI norms: a comment.

This note shows that evidence considered by Wooten (1984) to support claims of diagnostic superiority of standard over local MMPI norms, may mainly reflect the fact that a large proportion of the group tested by Wooten's consisted of persons with emotional, behavioral problems. Reevaluation of Wooten's data suggests a range of conditions under which Wooten's diagnostic criterion used with local norms is superior to the same criterion used with standard norms, and another range of conditions under which this criterion used with either local or standard norms is inferior to base rates.

Journal Article↗

Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene.

The structure of the Escherichia coli gene coding for the metabolically stable 4.5 S RNA has been determined by cloning and DNA sequence analysis. Results from Southern hybridization assays carried out prior to cloning show the 4.5 S DNA to be limited to a single locus in the E. coli K12 genome. A 5.4 X 10(3) base DNA fragment containing the 4.5 S DNA was cloned into plasmid pBR322 for restriction, hybridization and sequence analyses. Cells harboring the cloned gene overproduce the 4.5 S RNA by 15-fold under normal culturing conditions; however, no effect on growth rate is observed. DNA sequencing revealed only one copy of the 4.5 S RNA gene, with a deduced RNA sequence both longer at 114 bases and slightly different from the RNA sequence reported earlier. A promoter structure immediately preceding the structural gene shows good agreement with the prokaryotic consensus sequence at both the -35 and -10 regions. In addition, a G + C-rich sequence between the Pribnow box and the start of transcription agrees well with an apparent consensus sequence found for other stable RNA genes also under stringent control. No clearly recognizable termination signal was found immediately downstream from the 3' terminus of the 4.5 S DNA, although structural elements with that potential appear to occur. A potential coding sequence for a protein occurs about 100 bases downstream from the 4.5 S DNA, suggesting the possibility of a dual function 4.5 S RNA-mRNA transcript.

Base Sequence↗

Covalent crosslinking of Escherichia coli phenylalanyl-tRNA and valyl-tRNA to the ribosomal A site via photoaffinity probes attached to the 4-thiouridine residue.

tRNAPhe and tRNAVal of Escherichia coli were derivatized at the S4U8 position with p-azidophenacyl and p-azidophenacylacetate photoaffinity probes. The modified tRNAs could still function efficiently in all of the partial reactions of protein synthesis except for an approximately sevenfold decrease in the rate of translocation. Irradiation (310 to 340 nm) of probe-modified Phe-tRNA or Val-tRNA placed in the ribosomal A site led to crosslinking that was totally dependent on irradiation, the presence of the azido group on the probe, mRNA, and elongation factor Tu (EFTu). Prephotolysis of the modified tRNA abolished crosslinking, but prephotolysis of the ribosomes and factors had little effect. Crosslinking was efficiently quenched by mercaptoethanol or dithiothreitol, demonstrating accessibility of the probe to solvent. Use of GDPCP in place of GTP also blocked crosslinking, probably because of the retention of EFTu on the ribosome. Crosslinking with the p-azidophenacyl acetate (12 A) probe was only half as efficient as with the p-azidophenacyl (9 A) probe, and this ratio was not changed by varying Mg2+ from 5 to 15 mM. The crosslink was from a functional A site, since AcPhePhe-tRNA at the A site could be crosslinked, and it was A site-specific, because neither translocation nor direct non-enzymatic P site binding yielded any significant covalent product. The crosslink was to ribosomal protein(s) of the 30 S subunit. No other ribosomal component was crosslinked. Identification of the protein crosslinked is described in the accompanying paper.

Affinity Labels↗

Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs.

A plasmid containing a gene for the most abundant Escherichia coli leucine isoacceptor tRNA, tRNALeu1 (anticodon CAG) was isolated from the Clarke-Carbon bank of cloned E. coli DNA. The clone contains a 12.3-kilobase DNA insert which was mapped by F' DNA hybridization analysis to the region 82 to 89 min on the chromosome. The cloned tDNALeu corresponds to the minor of two chromosomal regions containing different amounts of DNA complementary to tRNALeuCAG . Sequencing of the tDNA region revealed it to contain a multimeric transcription unit consisting of four different tRNA genes. The genes are in the arrangement 5'-leader- tRNAArgCCG -57 base pairs- tRNAHisGUG -20 base pairs- tRNALeuCAG -42 base pairs- tRNAProUGG -3'. Coordinate expression of the component tRNAs in vivo and the absence of intercistronic promoters indicated that all four tDNAs reside in the same operon. The tDNA sequence is bounded by a promoter element showing good agreement with the procaryotic consensus sequence and a GC-rich stem-loop element that corresponds to a rho-independent terminator. The promoter region contains a GC-rich sequence that agrees with a suggested consensus stringency control element and two domains possessing dyad symmetry which flank the Pribnow box and include the putative stringency control region.

Base Sequence↗