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Biomedical subjects

T Kaplan

Publications and source records attributed to T Kaplan.

At least 19 recordsLinked to original sources
PubMed2006

Matrix metalloproteinase-9 in broncho-alveolar lavage fluid of patients with non-small cell lung cancer.

AIM: To evaluate concentration of MMP-9 in blood plasma and broncho-alveolar lavage fluid (BALF) from patients with non-small cell lung cancer (NSCLC). METHODS: Blood plasma from 40 NSCLC patients and 40 healthy donors was collected and concentrations of blood plasma and BALF MMP-9 were measured using ELISA. Correlation between MMP-9 level and gender, histological type of tumor and stage of disease was analyzed. RESULTS: Levels of blood plasma MMP-9 were significantly higher in NSCLC patients (p < 0.0001) then in control group, and were especially high in patients with stage IV of disease (stage I vs stage IV - p < 0.005, stage II vs stage IV - p < 0.01, stage III vs stage IV - p < 0.01). Also, stage IV of NSCLC was characterized by the highest level of BALF MMP-9 (stage I vs stage IV - p < 0.002, stage II vs stage IV p < 0.002, and stage III vs stage IV p < 0.007). Correlation between blood plasma and BALF MMP-9 levels and gender or histological type of tumor was insignificant. CONCLUSION: Our data revealed significant correlation between tumor stage and BALF and plasma MMP-9 levels in NSCLC patients.

Adult↗
PubMed2004

CIS: compound importance sampling method for protein-DNA binding site p-value estimation.

MOTIVATION: A key aspect of transcriptional regulation is the binding of transcription factors to sequence-specific binding sites that allow them to modulate the expression of nearby genes. Given models of such binding sites, one can scan regulatory regions for putative binding sites and construct a genome-wide regulatory network. In such genome-wide scans, it is crucial to control the amount of false positive predictions. Recently, several works demonstrated the benefits of modeling dependencies between positions within the binding site. Yet, computing the statistical significance of putative binding sites in this scenario remains a challenge. RESULTS: We present a general, accurate and efficient method for computing p-values of putative binding sites that is applicable to a large class of probabilistic binding site and background models. We demonstrate the accuracy of the method on synthetic and real-life data. AVAILABILITY: The procedure for scanning DNA sequences and computing the statistical significance of putative binding site scores is available upon request at http://compbio.cs.huji.ac.il/CIS/ CONTACT: nir@cs.huji.ac.il.

Algorithms↗
PubMed2000

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

The PSI-BLAST algorithm has been acknowledged as one of the most powerful tools for detecting remote evolutionary relationships by sequence considerations only. This has been demonstrated by its ability to recognize remote structural homologues and by the greatest coverage it enables in annotation of a complete genome. Although recognizing the correct fold of a sequence is of major importance, the accuracy of the alignment is crucial for the success of modeling one sequence by the structure of its remote homologue. Here we assess the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis. Each protein sequence is compared to a nonredundant database of the protein sequences by PSI-BLAST. Whenever a pair member detects its pair-mate, the positions that are aligned both in the sequential and structural alignments are determined, and the alignment sensitivity is expressed as the percentage of these positions out of the structural alignment. Fifty-two sequences detected their pair-mates (for 16 pairs the success was bi-directional when either pair member was used as a query). The average percentage of correctly aligned residues per structural alignment was 43.5+/-2.2%. Other properties of the alignments were also examined, such as the sensitivity vs. specificity and the change in these parameters over consecutive iterations. Notably, there is an improvement in alignment sensitivity over consecutive iterations, reaching an average of 50.9+/-2.5% within the five iterations tested in the current study.

Algorithms↗
PubMed2000

Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold.

Sequence comparison of proteins that adopt the same fold has revealed a large degree of sequence variation. There are many pairs of structurally similar proteins with only a very low percentage of identical residues at structurally aligned positions. It is not clear whether these few identical residues have been conserved just by coincidence, or due to their structural and/or functional role The current study focuses on characterization of STructurally Aligned Identical ResidueS (STAIRS) in a data set of protein pairs that are structurally similar but sequentially dissimilar. The conservation pattern of the residues at structurally aligned positions has been characterized within the protein families of the two pair members, and mutually highly and weakly conserved positions of STAIRS could be identified About 40% of the STAIRS are only moderately conserved, suggesting that their maintenance may have been coincidental. The mutually highly conserved STAIRS show distinct features that are associated with protein structure and function: a relatively high fraction of these STAIRS are buried within their protein structures. Glycine, cysteine, histidine, and tryptophan are significantly over-represented among the mutually conserved STAIRS. A detailed survey of these STAIRS reveals residue-specific roles in the determination of the protein's structure and function.

Animals↗
PubMed1998

Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group.

The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 degrees C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S-23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant 'cereus' strains, is proposed. Isolates of the new species grow at 4-7 degrees C but not at 43 degrees C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T (= DSM 11821T).

Animals↗
PubMed1998

Marital conflict by proxy after father kills mother: the family therapist as an expert witness in court.

The father killing the mother leaves the children effectively without parents. The extended family from both sides will often intervene to offer a home for the children, or at least to have a say in what arrangements are made for the children and how they are to be brought up. Intensely competitive and hostile feelings between the opposing sets of relatives are commonly aroused, and the children may be caught up in a battle reminiscent of the conflict between their parents, which culminated in the death of their mother. I and my colleagues have, as a team, seen more than 300 children who have lost one parent at the hands of the other, and we have been involved in subsequent custody battles as expert witnesses. Based on this experience and using this context as an example, the issues for the family therapist as expert witness in adversarial Court proceedings are presented. A case is described that illustrates the theoretical exposition--including the effectiveness of family therapy from the witness box.

Adult↗
PubMed1998

A nursing fellowship--building leadership skills.

A postgraduate nursing fellowship helps future nursing leaders deal with constant change, focus on learning and development, think systemically and mobilize resources through team building and goal directedness. An administrative fellowship program helps to develop future leaders, with the skills necessary to assume key positions in health care. Core competencies--leadership criteria, roles of the fellow and preceptor, skills of the fellow and preceptor and fellowship projects--are described.

Clinical Competence↗
PubMed1996

Identification and purification of a family of dimeric major cold shock protein homologs from the psychrotrophic Bacillus cereus WSBC 10201.

Whole-cell protein patterns of a psychrotrophic Bacillus cereus strain from cultures grown at 7 and 30 degrees C were compared. This analysis revealed that at least three major proteins are expressed at a significantly higher rate at 7 degrees C than at 30 degrees C. The most abundant of these cold-induced proteins was a small polypeptide of 7.5 kDa, designated CspA, of B. cereus. In addition, four small proteins very similar in size to CspA were seen on both 7 degrees C and 30 degrees C two-dimensional protein gels. Immunoblot analysis using B. cereus anti-CspA antibodies indicated that the five proteins described above plus an additional sixth protein not visible on silver-stained two-dimensional gels are members of a B. cereus cold shock protein family. This hypothesis was corroborated by cloning and sequencing of the genes encoding five proteins of this family. The protein sequences deduced are highly similar and show homology to small procaryotic cold shock proteins and to the cold shock domain of eucaryotic Y-box proteins. Besides CspA, only one of the additional five CspA homologs was slightly cold inducible. In the presence of 100 mM NaCl, the two purified members of the protein family (CspA and CspE) elute as dimers at an apparent molecular mass of 15 kDa from a gel filtration column. At higher salt concentrations, they dissociate into their monomers. Their ability to bind to the ATTGG motif of single-stranded oligonucleotides was demonstrated by band shift analysis.

Adaptation, Physiological↗
PubMed1992

Plasma lipid levels in active and sedentary premenopausal females.

Cross-sectional data on 19 long-distance runners (LD), 17 aerobic dancers (AD), 19 recreational joggers (RJ), and 15 inactive controls (IC) were examined for cardiovascular endurance and determination of plasma lipoproteins. Subjects included premenopausal eumenorrheic females who were non-smokers and presently not using oral contraceptives. Results indicated that all groups were similar in age, height and weight. Only the AD group had a significantly lower percent body fat (p less than .001) than the other groups. The LD, AD and RJ groups had a significantly higher VO2max than the IC group (p less than .05), and the LD and AD groups had a significantly higher VO2max than the RJ group (p less than .05). Analysis of a one-day food log indicated that the only difference in diet among the groups was a significantly lower intake of total and monounsaturated fat in the AD group (p less than .05) and a significantly lower intake of carbohydrates in the IC group than the AD group (p less than .05). Analysis of plasma lipids revealed no significant differences in any lipid variables among the groups. These findings indicate that healthy premenopausal eumenorrheic females with similar physical characteristics also have similar plasma lipid profiles regardless of their physical activity level.

Adult↗
PubMed1992

Father kills mother: post-traumatic stress disorder in the children.

Results of a study of over 100 children whose father killed their mother have been summarized and principles for practice have been formulated. All children orphaned by the death of one parent at the other's hands should be seen as soon as possible in a child psychiatry department and assessed. An immediate crisis intervention will probably be needed if they witnessed the killing to prevent PTSD. Bereavement counselling will be helpful in most cases. The caretakers will need support and help with their own mourning. Placement, access and custody, compensation, seeing the body, attending the funeral and dealing with family conflict will all need consideration. Long-term follow-up and further research are recommended.

Bereavement↗