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PubMed2003

Coverage of protein sequence space by current structural genomics targets.

By its purest definition the ultimate goal of structural genomics (SG) is the determination of the structures of all proteins encoded by genomes. Most of these will be obtained by homology modeling using the structures of a set of target proteins for experimental determination. Thanks to the open exchange of SG target information, we are able to analyze the sequences of the current target list to evaluate the extent of its coverage of protein sequence space. The presence of homologous sequences currently either in the Protein Data Bank (PDB) or among SG targets has been determined for each of the protein sequences in several organisms. In this way we are able to evaluate the coverage by existing or targeted structural data for the non-membranous parts of entire proteomes. For small bacterial proteomes such as that of H. influenzae almost all proteins have homologous sequences among SG targets or in the PDB. There is significantly lower coverage for more complex organisms, such as C. elegans. We have mapped the SG target list onto the ProtoMap clustering of protein sequences. Clusters occupied by SG targets represent over 150,000 protein sequences, which is approximately 44% of the total protein sequences classified by ProtoMap. The mapping of SG targets also enables an evaluation of the degree of overlap within the target list. An SG target typically occupies a ProtoMap cluster with more than six other homologous targets.

Algorithms↗
PubMed1997

Complete nose coverage to prevent airborne contamination via nostrils is unnecessary.

Besides an atraumatic procedure, aseptic techniques during surgery have been suggested to have a positive impact on the predictability of osseointegration. To avoid an infection of the surgical field, coverage of the face of the patient (drapes) and nose (surgical mask, drape and plastic film) were advocated in order to reduce airborne infections and to prevent a contact contamination of instruments and gloves. Such a coverage, however, increases the feeling of claustrophobia when local anaesthesia is used and can lead to hypoxemia. The aim of the present study was to investigate whether the expired air via the nostrils could contribute to the contamination of the oral surgical field. Test blood agar plates were installed for 30 min under the nose of volunteers lying on a surgical table; once with full coverage of their nostrils, as indicated above, and once without. Simultaneously, control plates were installed on a table besides the patient to measure the basic contamination from the environment. All plates were incubated both aerobically and anaerobically. The number of colony forming units (c.f.u.) recorded on test plates after aerobic and anaerobic incubation were surprisingly low, with a mean score of 2.7 and 5.0 c.f.u. for the uncovered situation, and 2.5 and 3.3 c.f.u. for the covered situation, respectively. The control plates were infected by a nearly comparable number of bacteria (means ranging from 2.2 to 3.2). These findings indicate that covering nostrils by a mask and sterile adhesive plastic film is not essential in avoiding airborne microbial contamination. However, the use of a meshed nose guard to prevent contact with the highly contaminated nasal skin is highly recommended.

Adult↗
PubMed2003

Validation and clinical relevance of a novel scalp coverage scoring method.

BACKGROUND/AIMS: Distinctive patterns of defective scalp skin coverage or alopecia have been identified by clinicians but do not help measuring the dynamics of hair changes over time. Hence, we conceived the scalp coverage scoring (SCS) method that integrates cumulative changes of hair growth or loss. In this paper, we report the results of validation studies demonstrating that the SCS can be applied in real time in the clinic or on global photographs for evaluating the severity of androgenetic alopecia (AGA) of male subjects and for monitoring changes over time. METHODS: Different panels totalling 38 different male subjects with AGA were classified according to a modified Norwood-Hamilton scale and were evaluated with the SCS system (real time or global photographs). The contrast-enhanced phototrichogram method (CE-PTG), a refined non-invasive and validated analytical technique was used for calibration purposes. RESULTS: The real time SCS was correlated with SCS on global photographs. The inter- and intra-observer variation of SCS obtained on global photographs was less than 3%. The real time SCS was negatively correlated with the clinical staging of male pattern baldness according to the modified Norwood-Hamilton scale, confirming less scalp coverage in more severly affected subjects. In 12 male subjects with AGA, after SCS evaluation of the top of the head, a 1-cm2 central target site was explored with CE-PTG. There was a significant correlation of real time SCS with the percentage of thick anagen hair (r = 0.53; P < 0.08) and with the density of thin hair (r = -0.68; P < 0.02). Changes over time as documented on global photographs (18 subjects at baseline and after 12 and 60 months) were rated by a panel of independent experts (paired photographs) who were not blinded as to time. Randomised individual photographs were also examined one at a time for SCS. This procedure documents data obtained without control of baseline photographs and establishes blinding as to time. The changes calculated from SCS (after-baseline) were correlated (r = 0.9; P < 0.0001) with the rating of the panel of experts. CONCLUSIONS: When minimum technical precautions are taken prior to the scoring session, the main points of interest of the SCS method are: Non-invasive quantitative and reproducible technique. Measures dynamics of scalp hair growth and loss. Easily applied in the hair clinic.

Alopecia↗
PubMed2001

Effect of extended coverage of immunosuppressive medications by medicare on the survival of cadaveric renal transplants.

Between 1993 and 1995, Medicare extended its coverage of maintenance immunosuppression medications following renal transplantation from 1 to 3 years. We hypothesized that Medicare's extension of immunosuppressive coverage would improve graft survival among low-income transplant recipients. We merged patient-level clinical data from the USRDS-distributed UNOS registry of kidney transplants throughout the USA with median family income for each patient's ZIP code from the 1990 Census. We were able to merge median incomes to 10,837 first cadaveric renal transplants performed in 1992-93 and 16,732 performed in 1995-97. Each of these chronological cohorts was divided into two groups, those with family incomes above (high-income group) and those below (low-income group) $36,033. There were no differences in graft survival at 1 year based on income in either chronological era. However, when Medicare covered immunosuppression medications for just 1 year, the low-income group of 1-year graft survivors had a 4.5% lower graft survival at the end of 3 years post-transplant (p < 0.001). During the 1995-97 period, during which Medicare provided 3 years' immunosuppression coverage, the low-income and high-income groups had equivalent graft survival at 3 years post-transplant.

Cadaver↗
PubMed1985

The hostile media phenomenon: biased perception and perceptions of media bias in coverage of the Beirut massacre.

After viewing identical samples of major network television coverage of the Beirut massacre, both pro-Israeli and pro-Arab partisans rated these programs, and those responsible for them, as being biased against their side. This hostile media phenomenon appears to involve the operation of two separate mechanisms. First, partisans evaluated the fairness of the media's sample of facts and arguments differently: in light of their own divergent views about the objective merits of each side's case and their corresponding views about the nature of unbiased coverage. Second, partisans reported different perceptions and recollections about the program content itself; that is, each group reported more negative references to their side than positive ones, and each predicted that the coverage would sway nonpartisans in a hostile direction. Within both partisan groups, furthermore, greater knowledge of the crisis was associated with stronger perceptions of media bias. Charges of media bias, we concluded, may reflect more than self-serving attempts to secure preferential treatment. They may result from the operation of basic cognitive and perceptual mechanisms, mechanisms that should prove relevant to perceptions of fairness or objectivity in a wide range of mediation and negotiation contexts.

Hostility↗
PubMed2006

Low-coverage vaccination strategies for the conservation of endangered species.

The conventional objective of vaccination programmes is to eliminate infection by reducing the reproduction number of an infectious agent to less than one, which generally requires vaccination of the majority of individuals. In populations of endangered wildlife, the intervention required to deliver such coverage can be undesirable and impractical; however, endangered populations are increasingly threatened by outbreaks of infectious disease for which effective vaccines exist. As an alternative, wildlife epidemiologists could adopt a vaccination strategy that protects a population from the consequences of only the largest outbreaks of disease. Here we provide a successful example of this strategy in the Ethiopian wolf, the world's rarest canid, which persists in small subpopulations threatened by repeated outbreaks of rabies introduced by domestic dogs. On the basis of data from past outbreaks, we propose an approach that controls the spread of disease through habitat corridors between subpopulations and that requires only low vaccination coverage. This approach reduces the extent of rabies outbreaks and should significantly enhance the long-term persistence of the population. Our study shows that vaccination used to enhance metapopulation persistence through elimination of the largest outbreaks of disease requires lower coverage than the conventional objective of reducing the reproduction number of an infectious agent to less than one.

Animals↗
PubMed2004

Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome.

In fruit fly research, chromosomal deletions are indispensable tools for mapping mutations, characterizing alleles and identifying interacting loci. Most widely used deletions were generated by irradiation or chemical mutagenesis. These methods are labor-intensive, generate random breakpoints and result in unwanted secondary mutations that can confound phenotypic analyses. Most of the existing deletions are large, have molecularly undefined endpoints and are maintained in genetically complex stocks. Furthermore, the existence of haplolethal or haplosterile loci makes the recovery of deletions of certain regions exceedingly difficult by traditional methods, resulting in gaps in coverage. Here we describe two methods that address these problems by providing for the systematic isolation of targeted deletions in the D. melanogaster genome. The first strategy used a P element-based technique to generate deletions that closely flank haploinsufficient genes and minimize undeleted regions. This deletion set has increased overall genomic coverage by 5-7%. The second strategy used FLP recombinase and the large array of FRT-bearing insertions described in the accompanying paper to generate 519 isogenic deletions with molecularly defined endpoints. This second deletion collection provides 56% genome coverage so far. The latter methodology enables the generation of small custom deletions with predictable endpoints throughout the genome and should make their isolation a simple and routine task.

Animals↗
PubMed2005

Uptake of gas-phase nitric acid to ice at low partial pressures: evidence for unsaturated surface coverage.

The adsorption of gas-phase nitric acid onto water-ice surfaces at temperatures between 200 and 239 K has been studied over short time scales using a coated-wall flow tube coupled to a chemical ionization mass spectrometer. The nitric acid partial pressures used were between 10(-8) hPa and 10(-6) hPa, making this the first systematic study under partial pressure conditions present in the upper troposphere. Whereas previous findings using this technique have shown that the surface coverages are saturated at 2 to 3 x 10(14) molecules cm(-2) (referenced to the geometric surface area of the ice film) when partial pressures are larger than about 10(-7) hPa, the principal finding from this study is that the surface coverages are in the unsaturated regime at lower partial pressures. A conventional Langmuir adsorption isotherm describes the uptake in a quantitative manner while dissociative Langmuir isotherms that have been used in the past to model this process do not. The unsaturated surface coverages are strongly temperature dependent, in agreement with a number of field measurements of the nitric acid (or NOy) component of cirrus cloud particles. These laboratory results match those in the field better than do those measured at significantly higher partial pressures but, nevertheless, they still indicate somewhat greater uptake, particularly at higher temperatures.

Journal Article↗
PubMed1986

Content relevance and content coverage in tests of grammatical ability.

Three widely used tests of grammatical ability were evaluated for content-oriented test construction using two procedures. First, a decision-making model was developed to assist in judging the content relevance and coverage of each test using information provided by respective test authors. Second, a comprehensive model of the grammatical domain was applied to individual items on the tests so that descriptions and comparisons of their content domains could be made. Both evaluations showed inadequate content relevance and coverage for all three tests. The content domains of these tests were found deficient when judged against an external standard as well as when examined according to their own content specifications. The influence of inadequate content relevance and coverage on assessment and remediation is discussed.

Humans↗
PubMed2001

Reasons for variation in coverage in the NHS cervical screening programme.

In order to investigate reasons for variation in coverage of cervical screening, data from standard Department of Health returns were obtained for all Health Authorities for 1998/1999. Approximately 80% of the variation between health authorities is explained by differences in age distribution and area classification. Considerable differences between Health Authority and Office of National Statistics (ONS) population figures in City and Urban (London) areas for the age group 25-29 years and for City (London) for age group 30-34 years, suggest an effect of list inflation in these groups. Coverage as a performance indicator may be more accurately represented using the age range 35-64 years. Using this narrower age range, the percentage of health authorities meeting the 80% 5-year coverage target increases from 87% to 90%.

Adult↗
PubMed2002

Factors associated with coverage in community-directed treatment with ivermectin for onchocerciasis control in Oyo State, Nigeria.

Community-directed distribution with ivermectin (CDTI) has been adopted by the African Programme for Onchocerciasis Control (APOC) as its main strategy for achieving sustained high coverage in endemic communities. This article describes the coverage results achieved when CDTI was introduced in four local government areas of Oyo State, Nigeria. Using a household survey after the second distribution, researchers documented that 68.6% of the community overall received the drug, and as did 85.0% of those who were eligible (not pregnant, not sick and at least 5 years of age). Six factors were associated with having received ivermectin. Four were personal characteristics: being male, being at least 35 years of age, belonging to the Fulani ethnic minority, having taken the drug at a previous distribution. Two village characteristics were smaller size, as measured by number of houses, and use of the central place mode of distribution as opposed to house-to-house. In-depth interviews with village leaders and volunteer community-directed distributors (CDDs) and focus group discussions among villagers provided qualitative data to help interpret the findings. Women in many villages felt excluded from decision making. The concerns of migrant farm workers living in Yoruba farm settlements were not well understood by health staff or the majority population. The main factor associated with receiving the ivermectin was having received it before, and qualitative comments about side-effects and beliefs about orthodox drugs indicated that issues of personal preferences, not addressed in a household coverage survey, need to be explored further. The findings can provide guidance in re-orienting health workers to the importance of fostering participation and cohesion among all segments of the community, especially the inclusion of women and minority groups.

Adolescent↗
PubMed2002

Improving glandular coverage during prostate biopsy using a long-core needle: technical performance of an end-cutting needle.

OBJECTIVE: To compare the technical performance of a 33-mm core-length biopsy needle with that of the standard 18 mm needle, as many prostate cancers are isoechoic and in large prostates the tissue coverage with the 18 mm needle is inadequate. PATIENTS AND METHODS: A 33-mm core length BioPince VSL disposable needle (Amedic, Sweden) and a standard TruCut 18 mm needle (Medical Device Technology Inc., FL, USA) were used to take prostatic biopsies in two groups of 15 patients. The following variables were assessed for each group: mean core length, core quality, capsular coverage (one or both capsules within the specimen), and side-effects in the first week after biopsy (for the BioPince group, surveyed using a self-completed questionnaire). The results were compared with historical data from a group of 30 patients biopsied using the standard needle. RESULTS: For the BioPince and standard groups the mean (sd) core length was 19.4 (8.9) and 14.9 (5.1) mm, respectively. Four needles in the BioPince group failed to capture a sample, requiring needle replacement. The samples were fragmented in 15 of 90 (17%) and 41 of 90 (46%) biopsies in the BioPince and standard groups, respectively (P < 0.05). Specimens had both capsules present in five of 90 (6%) and four of 90 (4%), respectively. Within 7 days minor bleeding was the most common side-effect. Pain after biopsy was the only symptom showing a significant difference between the groups, at six of 15 and none (P = 0.001), respectively. The incidence of haematuria, haematospermia and rectal bleeding was similar in the two groups (P > 0.05), but fever more common (three vs none) in the BioPince group (P = 0.06). CONCLUSION: When set at a 33-mm stroke length, the BioPince needle increases the mean core length by 30%, with less fragmentation than a standard 18 mm needle. However, it has a significant failure rate for capture (27% needle replacement rate), slightly greater morbidity (pain and possibly fever) and shows no advantage in capsular coverage. Therefore, there are shortcomings with this end-cutting needle when used at 33 mm core length.

Aged↗
PubMed2003

[Free tissue transplantation for defect coverage of the dorsum of the hand: aesthetic and functional aspects].

BACKGROUND: Complex and large soft-tissue defects of the dorsum of the hand, which cannot be covered with skin grafts or local flaps have to be reconstructed by means of free tissue transplantation. The purpose of this study was to present our experience with free fasciocutaneous flaps and muscle flaps with split-thickness skin graft for defect coverage of the dorsum of the hand in eight patients. PATIENTS AND METHOD: Evaluation of eight patients who underwent coverage of the dorsum of the hand with free flaps during 1997 to 2001 is presented. Other treatment options are discussed. RESULTS: Average age of the patients was 57 years and average follow-up was 25 months. For defect coverage we used a later alarm flap in four cases, a gracilis muscle flap with split-thickness skin graft in three cases and a latissimus dorsi flap with split-thickness skin graft in one case. In five patients we performed an extensor tendon reconstruction. Three of those cases achieved a good, one a fair and one case had a bad functional result. In one patient we had a partial flap loss. Muscle flaps with skin graft revealed better esthetic results than fasciocutaneous flaps. CONCLUSION: Microvascular free-tissue transplantation has expanded our options, giving us the opportunity for more refinement in hand reconstruction and improving the standards for a successful outcome.

Adult↗
PubMed2003

Dorsal hand coverage with free serratus fascia flap.

In reconstructing a defect on the dorsum of the hand, with the extensor tendons exposed or even missing, functional, as well as cosmetic, goals are of major importance. The authors present three cases of extensor tendon reconstruction, combined with soft-tissue reconstruction, with the free serratus fascia flap, the connective tissue over the serratus muscle, for dorsal hand coverage. The flap consists of thin and well-vascularized pliable tissue, with gliding properties excellent for covering exposed tendons. It is based on the branches of the thoracodorsal artery, which are raised in the flap, leaving the long thoracic nerve intact on the serratus muscle. Coverage of the flap with split-thickness skin graft is done immediately. The free serratus fascia flap is an ideal flap for dorsal hand coverage when the extensor tendons are exposed, especially because of low donor-site morbidity.

Adult↗
PubMed2005

[Soft-tissue coverage of the hand using the posterior interosseous artery flap].

UNLABELLED: Significant trauma, severe bacterial infections and tumour resections of the hand are often complicated by primary or secondary soft-tissue defects. The Posterior Interosseous Artery Flap (PIA), described by Zancolli and Angrigiani in 1985 offers one possibility for soft-tissue coverage. In this abstract, we present the results of 35 patients who were treated with distally based PIA flap reconstructions during the years 1998 to 2003. 24 patients were available for one-year follow-up and beyond. RESULTS: Long-term follow-up demonstrates excellent colour and texture match with reliable soft-tissue coverage. Two of the 33 flaps were lost because of ischemic necrosis. The incidence of distal local ischemia was predictable when the flaps were extended to the level of the PIP joint or beyond. CONCLUSION: The PIA flap affords a very durable and aesthetic option for soft-tissue coverage of the dorsum of the hand. The flap donor site can usually be closed primarily with little to no morbidity. In comparison to other local and distally based flaps such as the radial forearm flap, major blood vessels are spared. In summary, the PIA flap should be considered as a reliable and judicious alternative to free microvascular transfer procedures for soft-tissue defects of the hand proximal to the level of the PIP joint.

Adolescent↗
PubMed2005

[Defect coverage of the hand with the free serratus fascial flap].

PURPOSE: Coverage of exposed functional structures such as tendons, bones, vessels or nerves at the dorsal and palmar surface of the hand requires thin, supple tissue to provide adequate range of motion and a satisfying aesthetic result. Free fascial flaps are possible alternatives to cutaneous, fasciocutaneous and muscle flaps. The purpose of this retrospective study was to evaluate the functional and aesthetic results after coverage of the hand with free serratus fascial flaps in our department. METHOD AND CLINICAL MATERIAL: From 1994 to 2002, ten patients underwent free fascial flap coverage of the hand with eleven serratus fascial flaps. Six patients could be re-examined and answered a questionnaire about their satisfaction with the functional and aesthetic results. The mean follow-up was after 34 months. RESULTS: Average active range of motion of the hand, functional improvement and the aesthetic result were satisfying in all follow-up patients. No secondary debulking or other contouring procedures were required. CONCLUSION: We recommend the use of free serratus fascial flaps as a valuable alternative to fasciocutaneous or muscle flaps since the functional results are excellent; no additional procedures were necessary and the aesthetical results are appealing.

Adult↗
PubMed2006

Protective coverage of the median nerve using fascial, fasciocutaneous or island flaps.

PURPOSE: The aim of the study is to present our experience with fascial or fasciocutaneous pedicle and island flaps in the treatment of recurrences of CTS with and without median nerve lesions. MATERIAL AND METHODS: From 1987 to 2006 we have operated on 25 patients (17 women and 8 men, ages ranging from 38 to 76 years with a mean age of 55 years) due to a recurrence of CTS. All the patients required nerve coverage using a local or distant flap. There were 19 hypothenar fat flaps; two forearm radial artery flaps, a forearm ulnar artery flap, an ulnar fascial-fat flap and a posterior interosseous flap. Patients were clinically and instrumentally evaluated before the operation. Assessments of the evaluation parameters were classified in excellent, good, fair and poor according to clinical and return to work criteria. RESULTS: Patients were evaluated after a mean follow-up of 51 months (12 to 168 months). The pain evaluation showed an improvement passing from a mean value of 9 to 4. The best results were for those patients in whom the median nerve was undamaged (mean value of 1). Eleven patients obtained excellent results; good results were obtained in twelve cases; two patients demonstrated fair results due to partial median nerve injury. In these cases, a hypothenar fat flap and an ulnar fascial-fat flap were used, respectively. CONCLUSION: Protective coverage of the median nerve by using fascial or fasciocutaneous flaps after failure of CTR and/or unsuccessful re-operations is a good solution to furnish to the median nerve a gliding tissue to avoid adherences with the surrounding tissue of previous surgery. The protection of the nerve can reduce painful symptoms even if it does not permit a return to a painless condition. However, the clinical results in terms of median nerve functional recovery cannot be predicted: if the median nerve is damaged, protective coverage of it by flaps cannot give a favourable result in terms of recovery of both sensory and motor deficits.

Adult↗
PubMed1992

Cigarette advertising and magazine coverage of the hazards of smoking. A statistical analysis.

BACKGROUND: Health professionals have charged that magazines that depend on revenues from cigarette advertising are less likely to publish articles on the dangers of smoking for fear of offending cigarette manufacturers. Special concern has focused on magazines directed to women. Restricted coverage of smoking hazards could lead readers to underestimate the risks of smoking in relation to other health risks. METHODS: Using logistic-regression analysis of a sample of 99 U.S. magazines published during 25 years (1959 through 1969 and 1973 through 1986), we analyzed the probability that the magazines would publish articles on the risks of smoking in relation to whether they carried advertisements for cigarettes and in relation to the proportion of their advertising revenues derived from cigarette advertisements. We controlled for other factors that might influence coverage. RESULTS: The probability of publishing an article on the risks of smoking in a given year was 11.9 percent for magazines that did not carry cigarette advertisements, as compared with 8.3 percent for those that did publish such advertisements (adjusted odds ratio, 0.73; 95 percent confidence interval, 0.42 to 1.30). For women's magazines alone, the probabilities were 11.7 percent and 5.0 percent, respectively (adjusted odds ratio, 0.13; 95 percent confidence interval, 0.02 to 0.69). When the proportion of revenues derived from cigarette advertising was the independent variable, the probability of publishing an article on the risks of smoking in a given year was reduced by 38 percent (95 percent confidence interval, 18 percent to 55 percent) for magazines with the average proportion of total advertising revenues derived from cigarette advertising for the entire sample of magazines (6 percent) as compared with magazines with no cigarette advertising. This relation was particularly strong in the case of women's magazines. An increase of 1 percent in the share of advertising revenue derived from cigarette advertisements decreased the probability of covering the risks of smoking by three times as much as in other magazines. CONCLUSIONS: This study provides strong statistical evidence that cigarette advertising in magazines is associated with diminished coverage of the hazards of smoking. This is particularly true for magazines directed to women.

Advertising↗