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SYNOPSIS: Responder analyses are methods for analyzing randomized controlled trials, which purport to identify individuals or subgroups of study participants who experienced a "clinically meaningful" improvement from a treatment. Unfortunately, responder analyses have numerous methodological shortcomings, which preclude inferences concerning individual response to treatments and, thus, adoption into clinical practice. In this Viewpoint, we summarize 2 major limitations of responder analyses: (1) their thresholds of success involve arbitrary criteria and (2) responder analyses do not capture true individual treatment effects. J Orthop Sports Phys Ther 2023;53(XX):1-3. Epub: 20 June 2023. doi:10.2519/jospt.2023.11853 .

Purpose: This case report assesses gaze stability, postural control, and balance pre- and post-physical therapy intervention, including vestibular rehabilitation, in a 4-year-old child with posterior fossa syndrome following gross total resection of a juvenile astrocytoma brain tumor., Summary of Key Points: The child in this case study had improved balance and gaze stability, as determined by the Pediatric Balance Scale and the Dynamic Visual Acuity test upon completion of the 10-week intervention. STATEMENT OF CONCLUSION AND RECOMMENDATIONS FOR CLINICAL PRACTICE:: This case provides preliminary support of the need for vestibular screening in children with a diagnosis of posterior fossa syndrome. The success of the intervention suggests that vestibular rehabilitation exercises can be modified for use in preschool-aged children, and the specific intervention outlined in this case report can be easily replicated in a variety of treatment settings.

Ultraconserved elements (UCEs) are DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and located in syntenic positions in at least two genomes. Although hundreds of UCEs have been found in animal genomes, little is known about the incidence of ultraconservation in plant genomes. Using an alignment-free information-retrieval approach, we have comprehensively identified all long identical multispecies elements (LIMEs), which include both syntenic and nonsyntenic regions, of at least 100 identical base pairs shared by at least two genomes. Among six animal genomes, we found the previously known syntenic UCEs as well as previously undescribed nonsyntenic elements. In contrast, among six plant genomes, we only found nonsyntenic LIMEs. LIMEs can also be classified as either simple (repetitive) or complex (nonrepetitive), they may occur in multiple copies in a genome, and they are often spread across multiple chromosomes. Although complex LIMEs were found in both animal and plant genomes, they differed significantly in their composition and copy number. Further analyses of plant LIMEs revealed their functional diversity, encompassing elements found near rRNA and enzyme-coding genes, as well as those found in transposons and noncoding DNA. We conclude that despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.

Study Design: Systematic review., Objective: To summarize the research on accuracy of individual clinical diagnostic signs and tests for the presence of temporomandibular disorder (TMD), and for the subclassifications affiliated with TMD., Background: Diagnosis of TMD through clinical diagnostic measures has been reported in many studies; however, few of these studies have identified individual clinical tests or signs that can aid in the diagnosis of TMD or differentiate between the subclassifications of TMD., Methods: Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for this review. Computerized and hand searches were completed to locate articles on the diagnostic accuracy of clinical tests and signs. To be considered for review, the study required (1) an assessment of individual clinical measures of TMD, (2) a report of the diagnostic accuracy of these measures, and (3) an acceptable reference standard for comparison. Quality assessment of studies of diagnostic accuracy (QUADAS) scores were completed on each selected article. Sensitivity and specificity and negative and positive likelihood ratios were calculated for each diagnostic test described., Results: The search strategy identified 131 potential articles, which were narrowed down to 7 that met the criteria for this review. After assessment using the QUADAS score, 3 of the 7 articles were of high quality. All 7 studies used tests to differentiate subclassifications of TMD. The 7 studies included (1) diagnostic tests/signs of joint sounds, (2) joint movements, or (3) clinically oriented pain measures. There were no studies that investigated TMD versus a competing, non-TMD condition., Conclusion: Only 3 studies presented in this literature review were of high quality. Because all of the included studies assessed diagnostic accuracy among subclassifications of individuals suspected of having TMD, the ability of any of these tests to distinguish between patients with TMD versus patients without TMD remains unknown. Because of the lack of clear findings indicating compelling evidence for clinical diagnosis of TMD, and because of the low quality of most of these studies, the data are insufficient to support or reject these tests., Level of Evidence: Diagnosis, level 2a-.

Accurate structural models of target proteins are an essential component to structure-based drug design methods. To aid in this effort, the sequential forward floating selection (SFFS) algorithm is being applied to protein structure prediction. This algorithm demonstrates a reasonable balance between optimity of feature selection and efficiency while using large datasets such as the protein databank (PDB). The resulting protein structure predictions will be used in a study of HIV-1 PR.

Background: Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1). SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches -- most of which are irrelevant to the researcher., Results: We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO) database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the yeast Pho4p binding sites, CACGTG and CACGTT. Also, a cross-species search is presented to illustrate how potential hidden correlations in genomic data can be quickly discerned. The findings in one species are used as a catalyst to discover something new in another species. These experiments also demonstrate that our system performs well while searching multiple genomes -- without the main memory constraints present in other systems., Conclusion: We present a time-efficient algorithm to locate small segments of DNA and concurrently to search the annotation data accompanying the sequence. Genome-wide searches for short sequences often return hundreds of hits. Our experiments show that subsequently searching the annotation data can refine and focus the results for the user. Our algorithms are also space-efficient in terms of main memory requirements. Source code is available upon request.

Despite abundant library resources for many organisms, physical mapping of these organisms has been seriously limited due to lack of efficient library screening techniques. We have developed a highly efficient strategy for large-scale screening of genomic libraries based on multiplex oligonucleotide hybridization on high-density genomic filters. We have applied this strategy to generate a bacterial artificial chromosome (BAC) anchored map of mouse chromosome 11. Using the MIT mouse SSLP data, 320 pairs of oligonucleotide probes were designed with an "overgo" computer program that selects new primer sequences that avoid the microsatellite repeat. BACs identified by these probes are automatically anchored to the chromosome. Ninety-two percent of the probes identified positive clones from a 5.9-fold coverage mouse BAC library with an average of 7 positive clones per marker. An average of 4.2 clones was confirmed for 204 markers by PCR. Our data show that a large number of clones can be efficiently isolated from a large genomic library using this strategy with minimal effort. This strategy will have wide application for large-scale mapping and sequencing of human and other large genomes., (Copyright 1998 Academic Press.)

Germline mutations in the human MSH2, MLH1, PMS2 and PMS1 DNA mismatch repair (MMR) gene homologues appear to be responsible for most cases of hereditary non-polyposis colorectal cancer (HNPCC; refs 1-5). An important role for DNA replication errors in colorectal tumorigenesis has been suggested by the finding of frequent alterations in the length of specific mononucleotide tracts within genes controlling cell growth, including TGF-beta receptor type II (ref. 6), BAX (ref. 7) and APC (ref. 8). A broader role for MMR deficiency in human tumorigenesis is implicated by microsatellite instability in a fraction of sporadic tumours, including gastric, endometrial and colorectal malignancies. To better define the role of individual MMR genes in cancer susceptibility and MMR functions, we have generated mice deficient for the murine homologues of the human genes MLH1, PMS1 and PMS2. Surprisingly, we find that these mice show different tumour susceptibilities, most notably, to intestinal adenomas and adenocarcinomas, and different mutational spectra. Our results suggest that a general increase in replication errors may not be sufficient for intestinal tumour formation and that these genes share overlapping, but not identical functions.

Previously, we demonstrated induction of a unique macrophage prothrombinase, PCA, in MHV-3 infected BALB/cJ mice. By immunologic screening, a clone representing PCA was isolated from a cDNA library and sequenced. The sequence identified this clone as representing part of a gene, musfiblp, that encodes a fibrinogen-like protein. Six additional clones were isolated, and one clone, p11-3-1, encompassed the entire coding region of musfiblp. Murine macrophages did not constitutively express musfiblp, but when infected with MHV-3, synthesized musfiblp-specific mRNA. Musfiblp mRNA induction was earlier and significantly greater in BALB/cJ than A/J macrophages. Prothrombinase activity was demonstrate when musfiblp was expressed from p11-3-1 in RAW 264.7 cells. These data suggest that musfiblp encodes the MHV-induced prothrombinase.

We have analyzed the DNA released by sonication from avian nuclei, crosslinked with formaldehyde, by restriction mapping and equilibrium density gradient centrifugation. Our results indicate that regions flanking the adult beta-globin gene in adult reticulocytes have increased sensitivity to the mechanical shearing caused by sonication. These regions are near, and may overlap, the known nuclease hypersensitive regions that flank this gene. Like the hypersensitivity of these regions to nuclease digestion, the increased sensitivity to sonication is tissue-specific and appears to be due chiefly to the absence of nucleosome structures in these regions. Analysis of crosslinked chromatin fractionated by density gradient sedimentation suggests that DNA sequences near the matrix attachment region/enhancer element located 3' to the adult beta-globin gene are associated with transcriptionally-engaged chromatin fractions from both adult reticulocytes and day 5 chick embryo primitive erythroid cells. Sonication appears to be a useful tool for the study of chromatin structure.

The relationship between the postsynthetic modification of core histones by methylation and transcriptionally active chromatin was investigated in K562 erythroleukemia cells. Cells were incubated with L-[methyl-3H]methionine in the presence of cycloheximide. Under these conditions, only histones H3 and H4 were detectably methylated. Chromatin was fractionated by several methods, including low-salt elution, mononucleosome gel mobility shift using HPLC-purified HMG 17, and cesium chloride-guanidine equilibrium gradient centrifugation of formaldehyde-fixed chromatin. By these latter two methods, chromatin highly enriched for transcriptionally engaged or competent genes was isolated. A significant correlation was noted between postsynthetic modification of histones by methylation and by the slow-turnover form of acetylation. However, there was no enrichment of methylated histones in the transcriptionally competent fraction of chromatin isolated by HMG 17 binding. Moreover, only minor enrichment of methylated histone H3.1 and no enrichment of methylated histones H3.2 and H4 was detected in transcriptionally engaged chromatin isolated by gradient centrifugation. Chromatin soluble in low-salt buffer was found to be significantly enriched in methylated histones, but not in active genes. We conclude that histone methylation is associated with both transcriptionally active and transcriptionally inactive chromatin. The function of this modification, like that of bulk histone acetylation, remains to be determined.

We have previously shown that a cloned 480 bp DNA fragment that spans the 3'-enhancer region of the avian beta-globin gene cluster can become very tightly, perhaps covalently, bound to protein in avian nuclear matrices in vitro [Zenk et al. (1990) Biochemistry 29, 5221-5226]. This binding was not tissue-specific and was probably not mediated by topoisomerase enzymes. In the present study, we have examined avian nuclear matrices (or scaffolds) for the presence of very tight cellular DNA-protein complexes in the region of the beta-globin gene enhancer and of several other avian genes. Nuclear matrices were prepared by both high- and low-salt methods, and protein-DNA complexes were isolated by SDS/K+ precipitation after restriction enzyme digestion. In adult reticulocytes, up to 30% of the intact 3800 bp HindIII-EcoRI fragment that encompasses the beta-globin enhancer element may be very tightly bound to nuclear matrix protein. In adult avian thymus nuclei, the beta-globin enhancer is neither matrix-associated nor tightly bound to protein. In contrast, a 5.0-kb HindIII fragment of the malic enzyme gene is very tightly bound to nuclear matrix-associated protein in thymus cells, but not reticulocytes. The malic enzyme gene is active in thymus cells, and not in reticulocytes. These results suggests that certain regions of cellular DNA are very tightly, perhaps covalently, attached to nuclear matrix-associated proteins. Attachment follows a tissue-specific pattern that is associated with transcriptional activity.

The binding of HMG 17 to stripped core mononucleosomes containing DNA from the avian beta-globin gene cluster was examined to determine whether binding in vitro in this developmentally-regulated gene domain was associated with transcriptional activity or DNaseI-sensitivity in intact nuclei. Mononucleosomes were prepared from primitive and definitive stage embryonic red blood cells of chick embryos, adult reticulocytes, adult reticulocytes in which embryonic rho-globin transcription was induced, and adult thymus cells. Preferential binding by HMG 17 to mononucleosomes containing the beta-globin gene cluster was confined to erythroid-derived mononucleosomes that contain the embryonic rho-globin gene, the adult beta-globin gene, and DNA sequences located between these two genes, but not to those that contain the embryonic epsilon-globin gene. Comparison of these results to the known patterns of transcription and DNaseI-sensitivity within the beta-globin gene cluster shows that HMG 17 binding, although tissue-specific, does not correlate directly with either DNaseI-sensitivity or active gene transcription, but is dependent on other factors present in core mononucleosomes from this active gene domain.