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PubMed2006

Water as a lubricant for graphite: a computer simulation study.

The phase state and shear behavior of water confined between parallel graphite sheets are studied using the grand canonical Monte Carlo technique and TIP4P model for water. In describing the water-graphite interaction, two orientation-dependent potentials are tried. Both potentials are fitted to many-body polarizable model predictions for the binding energy and the equilibrium conformation of the water-graphite complex [K. Karapetian and K. D. Jordan in Water in Confining Geometries, edited by V. Buch and J. P. Devlin (Springer, Berlin, 2003), pp. 139-150]. Based on the simulation results, the property of water to serve as a lubricant between the rubbing surfaces of graphitic particles is associated, first, with the capillary condensation of water occurring in graphitic pores of monolayer width and, second, with the fact that the water monolayer compressed between graphite particles retains a liquidlike structure and offers only slight resistance to shear.

Journal Article↗
PubMed2000

Construction of hybrid peptide synthetases by module and domain fusions.

Nonribosomal peptide synthetases are modular enzymes that assemble peptides of diverse structures and important biological activities. Their modular organization provides a great potential for the rational design of novel compounds by recombination of the biosynthetic genes. Here we describe the extension of a dimodular system to trimodular ones based on whole-module fusion. The recombinant hybrid enzymes were purified to monitor product assembly in vitro. We started from the first two modules of tyrocidine synthetase, which catalyze the formation of the dipeptide dPhe-Pro, to construct such hybrid systems. Fusion of the second, proline-specific module with the ninth and tenth modules of the tyrocidine synthetases, specific for ornithine and leucine, respectively, resulted in dimodular hybrid enzymes exhibiting the combined substrate specificities. The thioesterase domain was fused to the terminal module. Upon incubation of these dimodular enzymes with the first tyrocidine module, TycA, incorporating dPhe, the predicted tripeptides dPhe-Pro-Orn and dPhe-Pro-Leu were obtained at rates of 0.15 min(-1) and 2.1 min(-1). The internal thioesterase domain was necessary and sufficient to release the products from the hybrid enzymes and thereby facilitate a catalytic turnover. Our approach of whole-module fusion is based on an improved definition of the fusion sites and overcomes the recently discovered editing function of the intrinsic condensation domains. The stepwise construction of hybrid peptide synthetases from catalytic subunits reinforces the inherent potential for the synthesis of novel, designed peptides.

Adenosine Triphosphate↗
PubMed1999

5S Ribosomal RNA Data Bank.

This paper presents the updated version of the data base of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA). This edition of the data bank contains 1889 primary structures of 5S rRNA and 5S rDNA. These include 60 archaebacterial, 439 eubacterial, 63 plastid, 9 mitochondrial and 1318 eukaryotic sequences. The nucleotide sequences of 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of organisms. The sequences stored in the database can be viewed and retrieved using the taxonomic browser at the URL: http://rose.man.poznan.pl/5SData/5SRNA.html++ +

Animals↗
PubMedDate not supplied

Elevated resting heart rate as a predictor of posttraumatic stress disorder after severe traumatic brain injury.

OBJECTIVE: This study indexed the relationship between resting heart rates (HRs) after injury and subsequent posttraumatic stress disorder (PTSD) in patients who sustained severe traumatic brain injury (TBI). METHODS: Patients who sustained a severe TBI (N = 68) had their resting HR assessed 1 week and 1 month after injury, and they were assessed for PTSD 6 months after injury with the PTSD Interview, a structured clinical interview based on the criteria of the Diagnostic and Statistical Manual of Mental Disorders, 3rd Edition, Revised. RESULTS: PTSD was diagnosed in 23% of patients. PTSD participants had higher HRs at 1 week but not at 1 month after trauma than non-PTSD participants. This difference remained significant when the effect of posttraumatic amnesia was controlled, but it was not significant when the effect of Glasgow Coma Scale was controlled. CONCLUSION: These findings accord with the proposal that fear conditioning can occur outside the level of awareness and contribute to PTSD development.

Adult↗
PubMed2006

A generative sketch model for human hair analysis and synthesis.

In this paper, we present a generative sketch model for human hair analysis and synthesis. We treat hair images as 2D piecewise smooth vector (flow) fields and, thus, our representation is view-based in contrast to the physically-based 3D hair models in graphics. The generative model has three levels. The bottom level is the high-frequency band of the hair image. The middle level is a piecewise smooth vector field for the hair orientation, gradient strength, and growth directions. The top level is an attribute sketch graph for representing the discontinuities in the vector field. A sketch graph typically has a number of sketch curves which are divided into 11 types of directed primitives. Each primitive is a small window (say 5 x 7 pixels) where the orientations and growth directions are defined in parametric forms, for example, hair boundaries, occluding lines between hair strands, dividing lines on top of the hair, etc. In addition to the three level representation, we model the shading effects, i.e., the low-frequency band of the hair image, by a linear superposition of some Gaussian image bases and we encode the hair color by a color map. The inference algorithm is divided into two stages: 1) We compute the undirected orientation field and sketch graph from an input image and 2) we compute the hair growth direction forthe sketch curves and the orientation field using a Swendsen-Wang cut algorithm. Both steps maximize a joint Bayesian posterior probability. The generative model provides a straightforward way for synthesizing realistic hair images and stylistic drawings (rendering) from a sketch graph and a few Gaussian bases. The latter can be either inferred from a real hair image or input (edited) manually using a simple sketching interface. We test our algorithm on a large data set of hair images with diverse hair styles. Analysis, synthesis, and rendering results are reported in the experiments.

Algorithms↗
PubMed2006

Adolescents and substance-related disorders: research agenda to guide decisions on Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-V).

AIMS: Since the publication of the Diagnostic and Statistical Manual of Mental Disorders fourth edition (DSM-IV), many studies have addressed substance use disorders (SUD) in adolescents. Based on that adolescent literature, this paper suggests further research to help guide decisions about revising for DSM-V the SUD criteria in DSM-IV. METHODS: The author has reviewed the 'Substance Related Disorders' section of DSM-IV-TR, recalled his experience in helping to draft that section, accessed relevant articles in PubMed and reviewed his own extensive file of literature citations. RESULTS: This paper suggests six questions for adolescent research to help guide the framers of DSM-V's 'Substance Related Disorders' section: (a) DSM-IV did not provide a diagnosis of cannabis withdrawal; should DSM-V continue that position? (b) Should SUD be included or referenced among 'Disorders Usually First Diagnosed in Infancy, Childhood, or Adolescence'? (c) Can inter-rater reliability of the substance abuse (SA) criteria be improved with altered example situations, text descriptions or phrasing of the current criteria? (d) Between ages 14 and 18 years is earlier onset of SUD a severity marker that could be incorporated into DSM-V as a predictor of worse course? (e) In DSM-V could a phenotypic descriptor of pathological multi-substance involvement document severity and predict course of SUD? (f) Could clinicians and patients benefit from DSM-V-related postpublication procedures for classifying emerging new drugs into DSM-V's categories? CONCLUSIONS: Without substantive changes in SA or substance dependence diagnostic criteria, research may improve the usefulness of those criteria for adolescents.

Adolescent↗
PubMed1988

TNM classification of genitourinary tumours 1987--position of the EORTC Genitourinary Group.

This report analyses the changes in the classification of the genitourinary tumours introduced by the 1987 edition of the TNM system. Criticism and suggestions for improvement are given. These are based on the extensive experience of the EORTC GU Group with clinical trial work particularly the identification of prognostic factors, on their success in reaching international consensus on tumour classification, and on information from the literature. Many of the changes introduced in the 1987 system are not considered to be strictly necessary. These include the introduction of the new additional descriptors, including "C" and "R", the changes in the T classification of prostatic and renal cancer, and the introduction of uniform N categories for all tumours and other features. We regret the omission of minimal requirements, the omission of the V classification for macroscopic or microscopic vascular invasion, the changes in the T categories of carcinoma of the bladder and the introduction of stage groupings for all urological tumours. Some of these changes are considered unacceptable. The attitude of the EORTC GU Group toward the use of the new TNM classification is indicated in detail.

Female↗
PubMed2006

The influence of depression, body mass index, and smoking on serum inhibin B levels in late reproductive-aged women.

CONTEXT: Women experiencing depression have difficult psychosocial functioning, and recent data suggest an earlier onset of menopause. Understanding the biological mechanism for the impairment of reproductive function associated with depression is important. OBJECTIVE: The objective of the study was to determine whether a lifetime history of depression is associated with reduced ovarian reserve as reflected in serum levels of the granulosa cell product, inhibin B. DESIGN: Residual serum samples from a subset of patients in the Harvard Study of Cycles and Moods were collected. SETTING: Patients were recruited from seven Boston-area communities. PATIENTS: Women with or without a history of major depression, based on structured clinical interviews for Diagnostic and Statistical Manual of Mental Disorders, fourth edition, were enrolled. A subset of patients who had provided an early follicular phase blood specimen at study enrollment and two or more other samples over the first 18-month period of follow-up were included. INTERVENTION: There were no interventions. MAIN OUTCOME MEASURE: Serum inhibin B levels were measured. RESULTS: Serum FSH levels were higher in women with a history of depression, whereas inhibin B levels did not differ between groups. Body mass index and age were significantly and inversely related to serum inhibin B levels. Smoking history was noted, for the first time, to have a significant negative association with inhibin B levels. CONCLUSIONS: Smoking has a direct negative effect on ovarian reserve, as suggested by decreased serum inhibin B levels. In contrast, effects of depression on the reproductive axis may occur at the level of the pituitary and/or hypothalamus rather than at the gonadal level, as suggested by increased serum FSH levels.

Adult↗
PubMed2004

Molecular phylogeny of the kidney-parasitic Sphaerospora renicola from common carp (Cyprinus carpio) and Sphaerospora sp. from goldfish (Carassius auratus auratus).

The genetic relatedness of two kidney-parasitic Sphaerospora species was studied. Although S. renicola, the causative agent of swimbladder inflammation of common carp fingerlings (Cyprinus carpio), and Sphaerospora sp. originating from goldfish (Carassius auratus auratus) were indistinguishable on the basis of spore morphology, they were found to be genetically different as their 18S rDNA sequences shared only 71.9% identical nucleotides. In the phylogenetic trees, Sphaerospora sp. from goldfish grouped with Myxidium truttae (AJ582061) within the clade of the coelozoic freshwater species. Sphaerospora renicola clustered with S. molnari (AF378345) within the group of myxosporeans histozoic in gills. The topology of the six Sphaerospora species on the phylogenetic trees implied that myxospore morphology does not correlate with the genetic relationships, and the genus seems to be polyphyletic.

Air Sacs↗
PubMedDate not supplied

New tools from the ACR (American College of Radiology): appropriateness criteria and utilization analysis.

Performing a clinically unnecessary study can cost a practice money under managed care and capitation contracts. The American College of Radiology (ACR) has developed two tools to help radiology facilities practice cost-efficient medicine without sacrificing quality of care: appropriateness criteria and utilization analysis. Appropriateness criteria were established by the ACR Board of Chancellors in 1993 to help imaging facilities determine appropriate imaging studies; these were first published in 1995; a subsequent edition will be published in 1996 and annually thereafter. Development of the criteria was based on Agency for Health Care Policy and Research guidelines. A task force which clinical conditions and variants were to be studied. The task force then performed a literature search. Members then reviewed the literature and reached a conclusion about the appropriateness of the various procedures. Because capitated contracts require some knowledge of the utilization of services, the ACR formed the utilization analysis committee in 1994. Facilities submit utilization data on a quarterly basis to the ACR. The data is then combined into both regional and national databases. These databases report back to the participating facilities, which can then compare themselves with other groups. All such information is confidential and is used for peer review only. A practice that participates in utilization analysis can view its own contract analysis, particularly in capitated contracts. Since many managed care organizations will not do business with a practice that hasn't performed this type of analysis, utilization analysis can be a way of winning contracts. Utilization analysis can also be a way to identify and control the risks that a practice has with managed care contracts. It offers the means for measuring a practice's performance against regional and national databases, and identifies areas of weakness. A practice is then able to take action to improve its quality of care in those areas.

Data Collection↗
PubMed1999

Ronald Ross and the malaria-mosquito cycle.

This essay examines briefly Ronald Ross's research on malaria in India between 1895 and 1899, during which time he elucidated the role of the Anopheles mosquito in the transmission of the disease. During his crucial experimental work in 1898, he used birds, human malaria being relatively uncommon in Calcutta. This article is based largely on the correspondence between Ross and Patrick Manson, which has just been edited.

Animals↗
PubMedDate not supplied

The Japanese database for the staging of lung cancer.

From the beginning of the 60s, Japanese Lung Cancer Society (JLCS) proposed an original TNM classification of lung cancer based on a database of resected cases. The final step was the UICC classification edited in 1973. Complete hilar-mediastinal lymph node dissection was started in the same era and the concept of station number of lymph nodes was introduced. The proposal of definition of "early lung cancer" came from Japan with the subgroups of hilar and peripheral type. A new national database is now collected for the next revision of UICC TNM classification to be edited in 2007.

Databases, Factual↗
PubMed1999

The Feasibility of Using Proteome Expression Profile for Genome Annotation.

By investigating into the expression data from ECO2DBASE (Edition 6),the feasibility of using proteome expression profile for genome annotation was tested. Based on our newly developed CRC (cellular role cluster) method,79 proteins extracted from ECO2DBASE were clustered into 4 CRCs. Function related proteins tend to be clustered into same CRC. Total 9 aminoacyl-tRNA synthetases were clustered into CRC2, whereas 4 heat-shock proteins into CRC3. These results indicate with enough proteome expression data and the efficient algorithm, proteome expression profile can provide very important information for genome annotation, while this kind of information is sequence-independent.

Journal Article↗
PubMed2004

Nursing contributions to the elimination of health disparities among African-Americans: review and critique of a decade of research.

The excessive burden of disease experienced by African-Americans has long been described by authorities in the public, private, and professional sector as a national health concern. Several reports have been published in the peer-reviewed literature that describe the outcomes of nurse-directed studies aimed at addressing the factors associated with the disparities experienced by African-Americans and these reports were also aimed toward the design of interventions to reduce and/or eliminate them. However, little is known about the scope, quality, and impact of these efforts relative to the promotion of health and the prevention of disease among African-American population groups. This report presents the results of a review, analysis, and critique of reports of outcomes of nursing research aimed toward reducing health-related disparities among African-Americans. These reports were described in a selected group of African-American nursing organizations and journals dedicated to providing a fonrum for the discussion of issues focused on cultual diversity, transcultural nursing, and multicultural health care issues. Included among the journals were the Journal of the National Black Nurses Association, the Journal of the Association of Black Nursing Faculty, the Journal of Chi Eta Phi Sorority, the Journal of Cultural Diversity, the Journal of Transcultural Nursing, and the Journal of Multicultural Nursing and Health. Results of the review, reported in two parts, the later of which will be reported in an upcoming edition, revealed that this body of nursing research provides the profession with a broad base of knowledge and insights. This knowledge is relative to the individual and familial impact of cardiovascular disease, cancer diabetes, HIV/AIDS, mental health and mental illness, and sickle cell disease within the African-American community. Knowledge and insights relative to the concerns and needs of childbearing, parenting, the elderly, caregivers and caregiving in African-American population groups is essential if health care disparities are to be truly eliminated. This review, analysis, and critique also revealed several gaps and limitations within this body of nursing research.

Black or African American↗
PubMed1988

Evaluation and management services in the Resource-Based Relative Value Scale.

Evaluation and management (E/M) services, which include making diagnoses, counseling and educating, developing strategies of care, and following up on treatment, are common to all medical specialties. Surveys of a variety of specialists using the magnitude-estimation method show that physicians agree closely in rating the work of particular E/M services. Regardless of the type of E/M service, the site at which it is performed, or the specialty performing it, work per unit of time varies only slightly. Comparison of work and time for services to which experts assigned billing codes in our consultative process indicates, however, that there may be large differences in the way different specialties use these billing codes. In some instances, work entailed by some of the E/M billing codes within specialties also appears to vary substantially. If empirical studies of physicians' coding and billing practices support our findings, possible responses might include (1) developing specialty-specific resource-based relative values for E/M services and (2) redefining the Physicians' Current Procedural Terminology, edition 4, codes for these services in terms that include time specifications.

Economics, Medical↗
PubMed1993

Analysis of embryonic development with a model for under- or overdispersion relative to binomial variation.

Observations from a study of the development of ovulations into embryos for Texel sheep are analysed with a model for count data that are under- or overdispersed relative to binomial variation. The analysis is based on maximum quasi-likelihood (McCullagh and Nelder, 1989, Generalized Linear Models, 2nd edition, London: Chapman and Hall), following an approach suggested by Williams (1982, Applied Statistics 31, 144-148). The dispersion parameter is developed as a combination of a variance component representing shared maternal effects and a correlation, typically negative, between ovulations within ewes. The number of ovulations (the binomial denominator) is included as an explanatory variable.

Androstenedione↗
PubMedDate not supplied

False positives, false negatives, and the validity of the diagnosis of major depression in primary care.

OBJECTIVE: To explore the issues of diagnostic specificity and psychiatric "caseness" (i.e., whether a patient meets the conditions to qualify as a "case" of a disease or syndrome) for major depression in the primary care setting. DESIGN: A cross-sectional study comparing the demographic, clinical, and mental health characteristics of patients identified as depressed by their family physicians with those meeting diagnostic criteria for major depression on the criterion standard Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Revised Third Edition. SETTING: The offices of 50 family physicians from private and academic practice in southeast Michigan. PATIENTS: A total of 1580 consecutive adult patients being seen for routine primary care services, from whom a weighted sample of 372 patients completed a set of mental health screening and diagnostic instruments. MAIN OUTCOME MEASURES: Patients were assigned to 1 of 4 groups (true positive, false positive, false negative, and true negative) based on clinician identification and Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Revised Third Edition diagnosis. Differences between the 4 groups in demographic and clinical characteristics, scores on mental health instruments and mental health history were explored. RESULTS: Physician identification of depression was strongly associated with increased familiarity with the patient and the presence of suggestive clinical cues, such as history of or treatment for depression, patient distress, and presence of vegetative symptoms. Patients in the false-positive group displayed significantly higher levels of distress and impairment and were significantly more likely to have a history of mental health problems and treatment than were those in the true-negative group. The 2 "misidentified" groups, false positives and false negatives, were indistinguishable in their clinical characteristics (impairment, distress, or mental health history). Both groups' scores occupied the middle ground between true positives and true negatives on most clinical characteristics. Physicians appeared to discriminate between these 2 groups on the basis of their knowledge of the patient's clinical history. CONCLUSIONS: Misidentification of depression in primary care may be in part an artifact of the use of the psychiatric model of caseness in the primary care setting. Our results are most consistent with a chronic disease-based model of depressive disorder, in which patients classified as false positive and false negative occupy a clinical middle ground between clearly depressed and clearly nondepressed patients. Family physicians appear to respond to meaningful clinical cues in assigning the diagnosis of depression to these distressed and impaired patients.

Adult↗
PubMed2002

Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

Algorithms↗