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PubMed2006

Genomic insights into positive selection.

The traditional way of identifying targets of adaptive evolution has been to study a few loci that one hypothesizes a priori to have been under selection. This approach is complicated because of the confounding effects that population demographic history and selection have on patterns of DNA sequence variation. In principle, multilocus analyses can facilitate robust inferences of selection at individual loci. The deluge of large-scale catalogs of genetic variation has stimulated many genome-wide scans for positive selection in several species. Here, we review some of the salient observations of these studies, identify important challenges ahead, consider the limitations of genome-wide scans for selection and discuss the potential significance of a comprehensive understanding of genomic patterns of selection for disease-related research.

Animals↗
PubMed2026

The genomic alchemist's arsenal: A comprehensive review of gene recruitment, regulatory rewiring, and the evolutionary arms race in snake envenomation.

Snake venom represents a striking example of evolutionary innovation, in which ancestral physiological gene networks have been co-opted into potent biochemical weapons. Advances in multi-omics, single-cell genomics, and structural bioinformatics have catalyzed a conceptual shift from descriptive toxin cataloging to a systems-level understanding of venom evolution, regulation, and function. This Review integrates genomic, cellular, and structural perspectives to delineate the molecular architecture underpinning venom diversification and target-site co-evolution. Emphasis is placed on regulatory mechanisms driving rapid expression plasticity, including super-enhancer activity, transposable element insertion, spatial heterogeneity within the venom gland, and non-coding RNA-mediated modulation. At the protein level, the review examines how hypervariable toxins engage in structural arms races with prey targets, and how multi-toxin complex formation, functional synergy, and molecular dynamics simulations inform models of lethality and resistance. A comparative framework is provided by contrasting high-potency predatory snake venoms with low-potency defensive venoms of hymenopterans such as bees and wasps, revealing how ecological selective pressures shape toxin potency, composition, and target specificity across taxa. Finally, current translational strategies are evaluated, with a focus on the relative merits of recombinant human monoclonal antibodies versus catalytic-site small-molecule inhibitors as deployable interventions for snakebite. By synthesizing evolutionary genomics, structural biology, comparative toxinology, and synthetic antivenomics, this Review outlines a predictive framework for anticipating venom evolutionary trajectories and for designing broad-spectrum, next-generation therapeutics.

Animals↗
PubMed2004

Pregnancy after kidney transplantation: an evidence-based approach.

Despite the relatively little space for transplantation in most medical schools, this issue is considered interesting by the students both for its clinical and ethical implications. The students were asked to choose a particular aspect of nephrology for a 2-hour case discussion. They chose the case of a 35-year-old female, kidney transplant recipient now 1.5 years postoperatively, who was coming to seek advice about pregnancy. The aim of the present work is to report an integration between narrative and evidence-based medicine (EBM) approaches. The search strategy was developed within a multidisciplinary working group, two of whose members were also masters in the methodology of systematic revisions. The first step in the discussion was the identification of ethical and methodological problem. In a rapidly developing field, books are unlikely to be able to give updated information. One needs to interact with electronic databases. In this context, no randomized controlled trial on pregnancy is expected. The evidence is likely to be heterogeneous. Prenatal care delivery differs around the world in part related to attitudes toward pregnancy, which depend upon religion and traditions. The second step was the definition of the search strategy. The third step, was selecting and cataloging the evidence. The titles and abstracts retrieved by the search strategy (272 items) were examined to identify full papers to be retrieved. The evidence retrieved was screened for the type of paper (reviews, primary studies, case reports, case series) and for the authors to give an indirect idea of duplicate publication bias. Teaching a complex and ever-changing subject, such as kidney transplantation, is a difficult task. The case of a young woman seeking information on the probability to undergo a successful pregnancy was particularly likely to exemplify the importance of being aware of the biases of the book-based information and on the need to interact with the internet. The search strategy developed by the working group of postgraduate trainees allowed students to have a direct experience with the complexity of the field. This preliminary study, as the basis for development of a checklist informed consent form on pregnancy in kidney transplantation, may give a first rough quantification of the work needed by a physician who wants to have a direct idea of the odds and risks of pregnancy in kidney transplant patients.

Evidence-Based Medicine↗
PubMed2006

Cost analysis of tumor downsizing for hepatocellular carcinoma liver transplant candidates.

We report the results of a prospective, intent-to-treat (ITT) trial on the costs of selective tumor downsizing (DS) before liver transplantation (LT) for patients affected with hepatocellular carcinoma (HCC). The trial started in January 1997 including adult patients with nodular-type HCC within and beyond the Milan criteria. Patients were downsized with transarterial chemoembolization (TACE), percutaneous ethanol injection (PEI) and/or radiofrequency ablation (RFA) according to clinical predictors. TACE and RFA were performed as inpatient procedures, while PEI was performed on an outpatient basis. Costs of DS were obtained according to the Tuscany Health Reimbursement Fee Catalog adjusted to yearly inflation rates from 1997 through 2005. Data analysis was performed at 1 year after the last enrollment of 198 patients, including 161 (81.3%) who were transplanted: 34 (17.2%) dropped out and 3 (1.5%) were still on the waiting list. One hundred and fifty-two patients (76.7%) underwent DS for a total of 201 procedures: 159 TACE, 39 PEI, and 3 RFA. Overall costs in Euros (euro) of waitlisting were 861,801.24 euro: 548,460 euro (63.7%) for pretransplantation evaluation; 197,994.84 euro (22.9%) for control visits and hospitalizations; and 115.346.4 euro (13.4%) for DS. Mean costs of DS were 758.58 euro +/- 270 euro per downstaged patient (747.53 euro +/- 257.1 euro Milan; 774.01 euro +/- 287.71 euro non-Milan); 582.85 euro +/- 398.87 euro per waitlisted patient (520.28 euro +/- 406.23 euro Milan; 520.28 +/- 364.48 euro non-Milan); and 716.4 euro per transplanted patient (580.67 euro Milan; 1026.76 euro non-Milan; +76.8%). A selective policy of tumor DS increased the costs of LT waitlisting by 13.4%, but due to higher dropout rates among non-Milan patients, the cost utility of DS was 76.8% higher in the Milan group.

Adolescent↗
PubMed2024

Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.

Several X-linked genes escape from X chromosome inactivation (XCI), while differences in escape across cell types and tissues are still poorly characterized. Here, we developed scLinaX for directly quantifying relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA sequencing (scRNA-seq) data. The scLinaX and differentially expressed gene analyses with large-scale blood scRNA-seq datasets consistently identified the stronger escape in lymphocytes than in myeloid cells. An extension of scLinaX to a 10x multiome dataset (scLinaX-multi) suggested a stronger escape in lymphocytes than in myeloid cells at the chromatin-accessibility level. The scLinaX analysis of human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes suggested the underlying impact of escape on the genotype-phenotype association. Overall, scLinaX and the quantified escape catalog identified the heterogeneity of escape across cell types and tissues.

X Chromosome Inactivation↗
PubMed2026

Pouria Salehi Nowbandegani.

Dr. Laura Zahn asked Dr. Pouria Salehi Nowbandegani about their study, "Defining and cataloging variants in pangenome graphs," and how they came to study this aspect of genomics.

Humans↗
PubMed2005

Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach.

High-density oligonucleotide arrays have become a popular assay for concurrent measurement of mRNA expression at the genome scale. Much effort has been devoted to the development of statistical analysis tools aimed at reducing experimental noise and normalizing experimental variation in gene expression analysis. However, these investigations do not detect or catalog systematic problems associated with specific oligonucleotide probes. Here, we present an investigation of problematic probes that yield consistent but inaccurate signals across multiple experiments. By evaluating data integrity among gene, probe sequence, and genomic structure we identified a total of 20,696 (10.5%) nonspecific probes that could cross-hybridize to multiple genes and a total of 18,363 (9.3%) probes that miss the target transcript sequences on the Affymetrix GeneChip U95A/Av2 array. The numbers of nonspecific and mistargeted probes on the U133A array are 29,405 (12.1%) and 19,717 (8.0%), respectively. The poor performance of the mistargeted probes was confirmed in two GeneChip experiments, in which these probes showed a 20-30% decrease in detecting present signals compared with normal probes. Comparison of qualitative expression signals obtained from SAGE and EST data with those from GeneChip arrays showed that the consistency of the two platforms is 30% lower in problematic probes than in normal probes. A Web application was developed to apply our results for improving the accuracy of expression analysis.

Expressed Sequence Tags↗
PubMed2005

Informatics for protein identification by mass spectrometry.

High throughput protein analysis (i.e., proteomics) first became possible when sensitive peptide mass mapping techniques were developed, thereby allowing for the possibility of identifying and cataloging most 2D gel electrophoresis spots. Shortly thereafter a few groups pioneered the idea of identifying proteins by using peptide tandem mass spectra to search protein sequence databases. Hence, it became possible to identify proteins from very complex mixtures. One drawback to these latter techniques is that it is not entirely straightforward to make matches using tandem mass spectra of peptides that are modified or have sequences that differ slightly from what is present in the sequence database that is being searched. This has been part of the motivation behind automated de novo sequencing programs that attempt to derive a peptide sequence regardless of its presence in a sequence database. The sequence candidates thus generated are then subjected to homology-based database search programs (e.g., BLAST or FASTA). These homology search programs, however, were not developed with mass spectrometry in mind, and it became necessary to make minor modifications such that mass spectrometric ambiguities can be taken into account when comparing query and database sequences. Finally, this review will discuss the important issue of validating protein identifications. All of the search programs will produce a top ranked answer; however, only the credulous are willing to accept them carte blanche.

Amino Acid Sequence↗
PubMed2006

Atomic resolution structures in nuclear transport.

There are currently at least 53 structures of components of nuclear transport in the Protein Databank. In addition to providing critical insights into molecular mechanisms of nuclear transport, these atomic resolution structures provide a large body of information that could guide biochemical and cell biological analyses involving nuclear transport proteins. This paper catalogs 53 crystal and NMR structures of nuclear transport proteins, with the emphasis on providing information useful for mutagenesis and overexpression of recombinant proteins.

Active Transport, Cell Nucleus↗
PubMed1998

PET radiopharmaceuticals: state-of-the-art and future prospects.

In this review we provide a conceptual overview of radiopharmaceuticals containing positron-emitting isotopes, not a catalog of radiopharmaceuticals or details of syntheses. We hope to provide an integrated framework for understanding the radiopharmaceuticals that are available at this time, describing both their strengths and weaknesses, and to look forward to some of the improvements that might be anticipated in the next decade. The range of biology that can be studied with positron emission tomography (PET) radiopharmaceuticals has greatly expanded, involving more sophisticated tracers and more sophisticated data analysis. PET measurements now encompass increasingly more specific aspects of human biochemistry and physiology as described in this review. As the biology being studied becomes more complex, the demands on the radiopharmaceutical and the methods of data analysis also become more complex. New synthetic chemistry and data analysis must develop in tandem. Radiopharmaceuticals must be designed to ensure that the rate determining step that is of interest is the one reflected in the data from the radiopharmaceutical. The challenge to the PET community of chemists, biologists, and physicians is to apply new knowledge of human biochemistry for developing and validating useful PET radiopharmaceuticals that will, in turn, produce useful nuclear medicine procedures. Initially the synthesis of a compound containing a short-lived radionuclide was a triumph in itself. However as the science advances the radiochemical synthesis becomes just the first step in a long trail that terminates in the compound being used to provide data on biological processes via a well-designed PET experiment. The resulting list of compounds and experiments should be as diverse as all of human biology and pathophysiology.

Brain↗
PubMed1997

Development needs of faculty in foodservice management.

OBJECTIVE: To determine the development needs of foodservice management (FSM) faculty originally prepared in other fields. DESIGN: Application of qualitative research methodologies to description and comparison of the perspective of three groups: faculty themselves, leaders in foodservice industry, and educators in advanced-degree programs. SUBJECTS: Purposive sampling of organization directories was used to recruit faculty members for two surveys (142 and 62 respondents) and four focus groups; 15 representatives from industry, professional organizations, and education (through an advisory committee); and 11 foodservice administration advanced-degree programs (through survey and study of program catalogs). MAIN OUTCOME MEASURES: Faculty competencies needed were compared from the three perspectives. STATISTICAL ANALYSES PERFORMED: Descriptive statistics plus chi 2 determinations were used to make comparisons. OUTCOMES: All three sources identified needs that could be classified into one of three groups: acquisition of theory, mastery of applications, and personal qualities. Theoretical groundwork needed included food science/quantity food production, financial and personnel management, marketing, customer satisfaction, and use of computer and other technologies. Although only 44% of faculty respondents had advanced degrees in FSM, their graduate study in other areas was applicable in meeting many of the competencies. Almost all faculty had some FSM industry experience-a high priority from all perspectives. CONCLUSIONS: Most faculty were involved in development activities and reported success in acquiring knowledge and application competence. The faculty members' lack of identification with FSM and their feelings of isolation were more problematic.

Data Collection↗
PubMed1998

Chronic fatigue syndrome and seasonal affective disorder: comorbidity, diagnostic overlap, and implications for treatment.

This study aimed to determine symptom patterns in patients with chronic fatigue syndrome (CFS), in summer and winter. Comparison data for patients with seasonal affective disorder (SAD) were used to evaluate seasonal variation in mood and behavior, atypical neurovegetative symptoms characteristic of SAD, and somatic symptoms characteristic of CFS. Rating scale questionnaires were mailed to patients previously diagnosed with CFS. Instruments included the Personal Inventory for Depression and SAD (PIDS) and the Systematic Assessment for Treatment Emergent Effects (SAFTEE), which catalogs the current severity of a wide range of somatic, behavioral, and affective symptoms. Data sets from 110 CFS patients matched across seasons were entered into the analysis. Symptoms that conform with the Centers for Disease Control and Prevention (CDC) case definition of CFS were rated as moderate to very severe during the winter months by varying proportions of patients (from 43% for lymph node pain or enlargement, to 79% for muscle, joint, or bone pain). Fatigue was reported by 92%. Prominent affective symptoms included irritability (55%), depressed mood (52%), and anxiety (51%). Retrospective monthly ratings of mood, social activity, energy, sleep duration, amount eaten, and weight change showed a coherent pattern of winter worsening. Of patients with consistent summer and winter ratings (n = 73), 37% showed high global seasonality scores (GSS) > or = 10. About half this group reported symptoms indicative of major depressive disorder, which was strongly associated with high seasonality. Hierarchical cluster analysis of wintertime symptoms revealed 2 distinct clinical profiles among CFS patients: (a) those with high seasonality, for whom depressed mood clustered with atypical neurovegetative symptoms of hypersomnia and hyperphagia, as is seen in SAD; and (b) those with low seasonality, who showed a primary clustering of classic CFS symptoms (fatigue, aches, cognitive disturbance), with depressed mood most closely associated with irritability, insomnia, and anxiety. It appears that a subgroup of patients with CFS shows seasonal variation in symptoms resembling those of SAD, with winter exacerbation. Light therapy may provide patients with CFS an effective treatment alternative or adjunct to antidepressant drugs.

Adult↗
PubMed1985

Oral contraceptives and cardiovascular disease: a critique of the epidemiologic studies.

Observational study designs used to investigate the relationship of oral contraceptive use to the occurrence of venous thromboembolism, stroke, myocardial infarction, and cardiovascular death include case-control, cohort, and mortality statistics studies. This analysis catalogs the findings of each of these epidemiologic studies, its statistical significance, and its performance with regard to scientific methodologic standards. An association between current oral contraceptive use and incidence of venous thromboembolism without predisposition has been consistently observed in case-control and cohort studies. Associations are less consistent for various types of stroke and for myocardial infarction. Only the Royal College of General Practitioners study found a significantly elevated risk of cardiovascular death with oral contraceptive use. The majority of mortality statistics studies offer little support for a relationship between oral contraceptive use and cardiovascular events. Major systematic problems in the epidemiologic studies include potential for bias in the detection of cardiovascular events and differences in the prognostic susceptibility of compared groups. Bias in the ascertainment of drug exposure is an unresolved issue for most of the case-control studies. Because of possible biases arising from methodologic deficiencies in these epidemiologic studies, questions as to the validity of the observed associations between oral contraceptive use and cardiovascular events should remain.

Australia↗
PubMed1998

Medication errors analysis is an opportunity to improve practice.

The United States Pharmacopeia (USP) Medication Errors Reporting (MER) Program collected and cataloged 2,213 reports between October 1991 and November 1996. Medication errors occur in all health care facilities, involve health care practitioners from all disciplines, and involve drugs from all categories, including neuromuscular blocking agents (38 out of 2,213). This class of drugs is discussed as an example of the program, and we trust will serve the reader as an educational guide about medication errors that occur with drugs in any class. When used inappropriately, they represent a higher morbidity and mortality than many other drug classes analyzed. Reports indicate various causes for the errors, such as similar-appearing products, and include suggestions by practitioners to prevent recurrence of the error. The USP Advisory Panel on Medication Errors has developed recommendations for facilities that are intended to prevent errors with neuromuscular blocking agents (NMB). The USP Medication Errors Reporting Program is presented in cooperation with the Institute for Safe Medication Practices (ISMP).

Adverse Drug Reaction Reporting Systems↗
PubMed1988

CAPA--Computer Aided Pesticide Analysis. Computer program for the automated evaluation of chromatographic data for residue analysis of foods.

Pesticide residue analysis in food by means of gas chromatography with columns of different polarity and several selective detectors provides the analyst with a great number of chromatographic data. The introduction of personal computer based chromatographic data systems into research laboratories increased the efficiency of information management and organization; user designed software packages now have direct access to the stored data. The computer program CAPA (Computer Aided Pesticide Analysis) was developed for the interpretation and evaluation of chromatographic results. The program is written in TURBO PASCAL 3.0 and consists of several subprograms. In the main database all pesticides are filed in a multidimensional structure. The various subprograms have access to this catalog of retention and response data. Using the subprogram INTERPRET, which is the core of CAPA, the analyst is provided with all information necessary to interpret a gas chromatogram: identification of calibrated pesticides and estimation of their concentration. Automated screening analyses can be evaluated with the subprogram AUTOINTERPRET, an automated of INTERPRET that uses all relevant information stored in the data base. A report is produced containing the pesticides found in the sample and proposals how to confirm them best with the equipment and methods available. Finally the analyst has to make the decision about the probable presence and quantity of the indicated pesticides and to project the next confirmatory step by using INTERPRET.

Autoanalysis↗
PubMed1996

Pleuropulmonary blastoma: a marker for familial disease.

OBJECTIVE: To catalog and evaluate patterns of disease in families of children with pleuropulmonary blastoma (PPB). METHODS: Data have been collected since 1988 on 45 children with PPB and their families. All pathologic materials were centrally reviewed. Preliminary molecular genetic analyses were performed when possible. RESULTS: In 12 of 45 patients, an association was found between PPB and other dysplasias, neoplasias, or malignancies in the patients with or in their young relatives. The diseases found to be associated with PPB include other cases of PPB, pulmonary cysts, cystic nephromas, sarcomas, medulloblastomas, thyroid dysplasias and neoplasias, malignant germ cell tumors, Hodgkin disease, leukemia, and Langerhans cell histiocytosis. Abnormalities of the p53 tumor suppressor gene, Wilms tumor suppressor gene (WT1), and the putative second genetic locus for Wilms tumor (WT2) were not found in preliminary investigations. CONCLUSIONS: The occurrence of PPB appears to herald a constitutional and heritable predisposition to dysplastic or neoplastic disease in approximately 25% of cases. All patients with PPB and their families should be investigated carefully. Further research of this new family cancer syndrome may provide insight into the genetic basis of these diseases.

Adult↗
PubMed1999

Developing a register for randomized controlled trials in prosthodontics: results of a search from prosthodontic journals published in the United States.

STATEMENT OF PROBLEM: Treatment decisions are often made despite absence of evidence from well-conducted clinical trials. Conclusions about treatment efficacy derived from nonexperimental approaches often overestimate treatment effect. Randomized controlled trials (RCTs) provide the most reliable basis for evaluating effectiveness of treatment interventions. PURPOSE: This study attempted to identify and catalog RCTs in prosthodontic journals published in the United States as an initial step in creating a register of clinical trials that would be a resource in setting up systemic overviews of prosthodontic literature. METHODS: The International Journal of Prosthodontics, The Journal of Prosthetic Dentistry, and The Journal of Prosthodontics published between 1988 and 1997 were searched manually to identify clinical trials. Clinical trials had to meet the following criteria for inclusion in the register: the trial must involve human subjects, must include at least 2 treatment groups, and treatment group allocation must be randomized. RESULTS: A total of 3,631 articles in 196 journal issues were screened. Sixty-two articles (1.7%) met the minimum criteria for inclusion in the RCT register. CONCLUSION: Given the lack of randomized controlled trials in prosthodontic journals, a concerted effort by the organized prosthodontic community should be made to screen national and international journals and contribute to the development of a register of randomized controlled trials relevant to prosthodontics.

Dental Research↗
PubMed2001

The legacy of pharmacogenetics and potential applications.

Some 40 years of pharmacogenetic research indicates that knowledge of human genetic diversity is essential to a broader understanding of variation in human drug response, and suggests that drug therapy tailored to the genetic characteristics of the individual may be a realistic goal. Aided by new technologies, molecular studies of genetic polymorphisms of many human enzymes, receptors, and other proteins indicate that only a limited number of important protein variants account for the diversity in drug response, raising the prospect that these variants may be cataloged relatively soon for many human populations. The next great challenge of pharmacogenetics is to pin down the cellular location and effect of these variant proteins on the pathways and networks that govern individual variation in responses to drugs and other exogenous chemicals. In this paper, we will discuss some the current challenges to progress in pharmacogenetics and newer strategies that might be used to improve prospects of drug design and personalized therapy.

Animals↗