bluuebunny/crossref_metadata_2025 huggingface dataset:
A theory for particle size segregation in shallow granular free-surface flows
Authors: Gray J.M.N.T , Thornton A.R
Published: May 2005

Granular materials composed of a mixture of grain sizes are notoriously prone to segregation during shaking or transport. In this paper, a binary mixture theory is used to formulate a model for kinetic sieving of large and small particles in thin, rapidly flowing avalanches, which occur in many industrial and geophysical free-surface flows. The model is based on a simple percolation idea, in which the small particles preferentially fall into underlying void space and lever large particles upwards. Exact steady-state solutions have been constructed for general steady uniform velocity fields, as well as time-dependent solutions for plug-flow, that exploit the decoupling of material columns in the avalanche. All the solutions indicate the development of concentration shocks, which are frequently observed in experiments. A shock-capturing numerical algorithm is formulated to solve general problems and is used to investigate segregation in flows with weak shear.
On the patterns of interaction between shear and interfacial modes in plane air–water Poiseuille flow
Authors: Shapiro Evgeniy , Timoshin Sergei
Published: May 2005

The current work deals with the numerical analysis of linear stability problems in a stratified plain Poiseuille flow of air over water with equal layer heights. The interaction and branch exchange between Tollmien–Schlichting instability in air and interfacial instability is discovered and investigated. This effect is shown to stabilize disturbances with wavelengths of the order of channel height for interfacial waves and to produce a closed stable region inside the neutral curve of the interfacial mode. The behaviour of three unstable modes in the problem, corresponding to Tollmien–Schlichting type instability in air and water layers and interfacial instability respectively, has been studied in detail. Neutral conditions for all three modes and the stable region have been calculated.
Molecular preservation in Late Cretaceous sauropod dinosaur eggshells
Authors: Schweitzer M.H , Chiappe L , Garrido A.C , Lowenstein J.M , Pincus S.H
Published: May 2005

Exceptionally preserved sauropod eggshells discovered in Upper Cretaceous (Campanian) deposits in Patagonia, Argentina, contain skeletal remains and soft tissues of embryonic Titanosaurid dinosaurs. To preserve these labile embryonic remains, the rate of mineral precipitation must have superseded post-mortem degradative processes, resulting in virtually instantaneous mineralization of soft tissues. If so, mineralization may also have been rapid enough to retain fragments of original biomolecules in these specimens. To investigate preservation of biomolecular compounds in these well-preserved sauropod dinosaur eggshells, we applied multiple analytical techniques. Results demonstrate organic compounds and antigenic structures similar to those found in extant eggshells.
A silicified bird from Quaternary hot spring deposits
Authors: Channing Alan , Schweitzer Mary Higby , Horner John R , McEneaney Terry
Published: May 2005

The first avian fossil recovered from high-temperature hot spring deposits is a three-dimensional external body mould of an American coot (
Fulica americana
) from Holocene sinters of Yellowstone National Park, Wyoming, USA. Silica encrustation of the carcass, feathers and colonizing microbial communities occurred within days of death and before substantial soft tissue degradation, allowing preservation of gross body morphology, which is usually lost under other fossilization regimes. We hypothesize that the increased rate and extent of opal-A deposition, facilitated by either passive or active microbial mediation following carcass colonization, is required for exceptional preservation of relatively large, fleshy carcasses or soft-bodied organisms by mineral precipitate mould formation. We suggest physico-chemical parameters conducive to similar preservation in other vertebrate specimens, plus distinctive sinter macrofabric markers of hot spring subenvironments where these parameters are met.
The geological history of deep-sea colonization by echinoids: roles of surface productivity and deep-water ventilation
Authors: Smith Andrew B , Stockley Bruce
Published: May 2005

The origins and geological history of the modern fauna of deep-sea echinoids is explored using a combination of palaeontological and molecular data. We demonstrate that, whereas generalist omnivores have migrated into the deep sea in low numbers over the past 200 Myr, there was a short time-interval between approximately 75 and 55 Myr when the majority of specialist detritivore clades independently migrated off-shelf. This coincides with a marked increase in seasonality, continental run-off and surface water productivity, and suggests that increasing organic carbon delivery into ocean basins was an important controlling factor. Oceanic anoxic events, by contrast, appear to have played a subsidiary role in controlling deep-sea diversity.
Habitat selection and ecological speciation in Galápagos warbler finches (
Certhidea olivacea
and
Certhidea fusca
)
Authors: Tonnis Brandon , Grant Peter R , Grant B. Rosemary , Petren Kenneth
Published: May 2005

We investigated phylogeographic divergence among populations of Galápagos warbler finches. Their broad distribution, lack of phenotypic differentiation and low levels of genetic divergence make warbler finches an appropriate model to study speciation in allopatry. A positive relationship between genetic and geographical distances is expected for island taxa. Warbler finches actually showed a negative isolation by distance relationship, causing us to reject the hypothesis of distance‐limited dispersal. An alternative hypothesis, that dispersal is limited by habitat similarity, was supported. We found a positive correlation between genetic distances and differences in maximum elevation among islands, which is an indicator of ecological similarity. MtDNA sequence variation revealed monophyletic support for two distinct species.
Certhidea olivacea
have recently dispersed among larger central islands, while some
Certhidea fusca
have recently dispersed to small islands at opposite ends of the archipelago. We conclude that females have chosen to breed on islands with habitats similar to their natal environment. Habitat selection is implicated as an important component of speciation of warbler finches, which is the earliest known divergence of the adaptive radiation of Darwin's finches. These results suggest that small populations can harbour cryptic but biologically meaningful variation that may affect longer term evolutionary processes.
Catalytic reduction of dinitrogen to ammonia at well-defined single metal sites
Authors: Schrock Richard R
Published: May 2005

Dinitrogen (N
2
) is reduced to ammonia at room temperature and 1 atm with molybdenum catalysts that contain tetradentate [HIPTN
3
N]
3−
triamidoamine ligands {[HIPTN
3
N]
3−
=[{3,5-(2,4,6-
i
-Pr
3
C
6
H
2
)
2
C
6
H
3
NCH
2
CH
2
}
3
N]
3−
, an example being [HIPTN
3
N]Mo(N
2
)} in heptane. Slow addition of the proton source ({2,6-lutidinium}{BAr′
4
}; Ar′=3,5-(CF
3
)
2
C
6
H
3
) and reductant (decamethyl chromocene) assure a high yield of ammonia (63–65% in four turnovers) versus dihydrogen formation. Numerous X-ray studies, along with isolation and characterization of seven intermediates in the proposed catalytic reaction (under noncatalytic conditions), suggest that N
2
is being reduced at a sterically protected, single Mo centre that cycles between states Mo(III), Mo(IV), Mo(V) and Mo(VI).
Active sites and states in the heterogeneous catalysis of carbon–hydrogen bonds
Authors: Somorjai Gabor A , Marsh Anderson L
Published: May 2005

C–H bond activation for several alkenes (ethylene, propylene, isobutene, cyclohexene and 1-hexene) and alkanes (methane, ethane,
n
-hexane, 2-methylpentane and 3-methylpentane) has been studied on the (111) crystal face of platinum as a function of temperature at low (<10
−6
 Torr) and high (≥1 Torr) pressures in the absence and presence of hydrogen pressures (≥10 Torr). Sum frequency generation (SFG) vibrational spectroscopy has been used to characterize the adsorbate structures and high pressure scanning tunnelling microscopy (HP-STM) has been used to monitor their surface mobility under reaction conditions during hydrogenation, dehydrogenation and CO poisoning. C–H bond dissociation occurs at low temperatures, approximately 250 K, for all of these molecules, although only at high pressures for the weakly bound alkanes because of their low desorption temperatures. Bond dissociation is known to be surface structure sensitive and we find that it is also accompanied by the restructuring of the metal surface. The presence of hydrogen slows down dehydrogenation and for some of the molecules it influences the molecular rearrangement, thus altering reaction selectivity. Surface mobility of adsorbates is essential to produce catalytic activity. When surface diffusion is inhibited by CO adsorption, ordered surface structures form and the reaction is poisoned. Ethylene hydrogenation is surface structure insensitive, while cyclohexene hydrogenation and dehydrogenation are structure sensitive.
n
-Hexane and other C
6
alkanes form either upright or flat-lying molecules on the platinum surface which react to produce branched isomers or benzene, respectively.
Activation of oxygen at metal surfaces
Authors: Carley A.F , Davies P.R , Roberts M.W
Published: May 2005

Oxygen chemisorption at metal surfaces has been shown through a combination of scanning tunnelling microscopy and photoelectron spectroscopy to involve transient states that provide low energy pathways for a wide range of surface reactions including the catalytic oxidation of ammonia and hydrocarbons. The kinetically ‘hot’ transients are disordered and mobile, become unreactive when they form ordered structures, and are characterized by non-classical kinetic behaviour.

The role of surface additives (caesium) in controlling oxygen structures and the implications of oxygen transients for theory and reaction mechanisms in applied catalysis are considered.
Influence of pH on Soil Charge Characteristics and Cadmium Sorption in Some Noncontaminated Soils of Indian Subtropics
Authors: Karak Tanmoy , Das Dilip Kumar , Singh Uttam Kumar , Maiti Debtanu
Published: May 2005

Concentrations of total dissolved cadmium (Cd) and activity of its free ions in soil solution are suggested to be influenced by soil pH, organic matter (OM) content, cation exchange capacity (CEC), and clay mineralogy. We investigated the sorption of Cd by taking 25-, 50-, and 100-µM Cd solutions in five noncontaminated soils of West Bengal, India, having differing chemical properties with batch sorption experiments. The charge characteristics and point of zero salt effect (PZSE) of all experimental soils were calculated by the potentiometric titration method measuring the adsorption of H+and OH–on amphoteric surfaces in solutions of varying ionic strength (I). Sorption of Cd was more pronounced at pH levels greater than PZSE for all experimental soils. The CEC, OM content, clay mineralogy, and specific surface area (SSA) also had a great influence on the sorption of Cd from soil solution to soils. The relationships of Cd with those parameters were found to be consistent and the results concluded that Cd sorption in soils is strongly affected by the soil characteristics.
Managing Scoliosis in a Young Child with Rett Syndrome: A Case Study
Authors: Lotan Meir , Merrick Joav , Carmeli Eli
Published: May 2005

Rett syndrome is a genetic disorder primarily affecting females. One of its most disabling features is the severe and rapid progression of scoliosis. So far, only surgical intervention has succeeded in reversing the development of scoliosis in Rett syndrome.The present study describes a new management approach implemented with a girl with Rett syndrome. The core of the management regime was intensive: asymmetrical activation of trunk muscles through equilibrium reactions. The X-rays accompanying the article (evaluated by four experienced orthopedic surgeons blinded to the intervention process) suggested that the intervention was successful in reversing the progress of the scoliosis for the above-mentioned child. Discontinuation of treatment led to severe and rapid deterioration of the spinal curve.Due to the fact that this was a case study, generalization is limited, but we suggest further investigation and studies with this method.
A Staphylococcus aureus mouse keratitis topical infection model: Cytokine balance in different strains of mice
Authors: Hume Emma BH , Cole Nerida , Khan Shamila , Garthwaite Linda L , Aliwarga Yulina , Schubert Tracey L , Willcox Mark DP
Published: May 2005

Staphylococcus is a leading cause of the potentially blinding disease microbial keratitis. Even with the use of antibiotic therapy, the host inflammatory response continues to damage the cornea, which may lead to blindness. Manipulation of the host response may help improve patient outcome from this devastating disease. We aim to understand the contribution of the host response to Staphylococcus aureus infection. A S. aureus keratitis mouse model was developed in both C57BL/6 and BALB/c mice using two different strains of S. aureus (8325‐4 and Staph 38). Twenty‐four hours postinfection, mice were killed and eyes were harvested for enumeration of bacteria, polymorphonuclear leucocytes, chemokines and cytokines. The laboratory strain 8325‐4 was not as virulent as the clinical isolate Staph 38. In vitro data showed a 250‐fold increase in invasion of human corneal epithelial cells by Staph 38 compared to 8325‐4. BALB/c mice were susceptible to S. aureus infection whereas C57BL/6 mice were resistant. The resistant C57BL/6 mice were polarized towards a Th2 response, which may be protective for these mice. IL‐4, IL‐10 and IL‐6 were elevated significantly in C57BL/6 mice infected with Staph 38 (P < 0.05). Macrophage inflammatory peptide (MIP)‐2 was also significantly elevated in C57BL/6 mice (P < 0.001). The susceptible BALB/c mice had a muted cytokine response, which suggests that S. aureus might be ‘walled off’ during infection and might avoid host defences. IL‐4, IL‐10 and IL‐6 cytokines may be protective during Gram‐positive corneal infection and therefore may be useful for adjunct therapies in the treatment of this disease.
Transfection of human monocyte‐derived dendritic cells with CpG oligonucleotides
Authors: Erhardt Michael , Gorschlüter Marcus , Sager Jens , Ziske Carsten , Strehl John , Lilienfeld‐Toal Marie V , Schmidt‐Wolf Ingo GH
Published: May 2005

Monocyte‐derived dendritic cells (mDC), the most frequently applied DC subset in clinical studies, which can be obtained easily from peripheral blood monocytes after incubation with GM‐CSF and IL‐4, have not been clearly demonstrated to be activated by CpG oligodeoxynucleotides (ODN). The development of novel molecular strategies – such as the use of CpG‐ODN – to increase immunological functions and thus improve the therapeutic efficiency of mDC vaccines in the treatment of malignant diseases is highly desirable. CpG‐ODN need to be internalized into specific intracellular compartments to be active. Therefore, we applied electroporation and lipofection and compared these techniques with incubation to overcome possible defects in localization. Conditions of CpG‐ODN transfection of these cells were optimized using fluorescein‐marked ODN 2216. We were able to achieve high transfection efficiencies with various methods of delivery. However, we did not observe increased expression of maturation‐associated and functionally relevant surface antigens (CD14, HLA‐DR, CD40, CD83, CD80 and CD86), significant secretion of IL‐12 and IFN‐α in culture supernatant, or enhanced antitumour activation of cytokine‐induced killer cells. In conclusion, our results show that non‐viral transfection of CpG‐ODN is not sufficient to overcome resistance of mDC to CpG activation.
Pollinator activity can explain variation in outcrossing rates within individual trees
Authors: HINGSTON ANDREW B. , POTTS BRAD M.
Published: May 2005

Abstract We tested the hypothesis that the previously recorded higher outcrossing rates and numbers of seeds per capsule from the upper, than from the lower, branches of trees ofEucalyptus globulus(Myrtaceae) is the result of greater pollinator activity in the upper parts of the canopy. Observations of bird pollinators on 23 trees, with flowers distributed evenly between the upper and lower halves of canopies, supported this hypothesis. Birds spent significantly more time foraging, and commenced foraging significantly more often, in the upper halves than in the lower halves of canopies. Flowers in the upper halves ofE. globuluscanopies would therefore be expected to receive more outcross‐pollen from bird pollinators because they are usually visited more often and would probably receive a greater ratio of outcross‐ to self‐pollen. We propose that such variation in pollinator activity and outcross‐pollen deposition results in different selective pressures on the mating system and pollination syndrome in different parts of the canopy. This may result in balanced selection for these traits, contributing to the maintenance of the mixed mating and generalized pollination systems ofE. globulus.
Effect of Race and Sex on Primary Care Physicians' Diagnosis and Treatment of Late‐Life Depression
Authors: Kales Helen C. , Neighbors Harold W. , Valenstein Marcia , Blow Frederic C. , McCarthy John F. , Ignacio Rosalinda V. , Taylor Kiran K.‐K. , Gillon Leah , Mellow Alan M.
Published: May 2005

Objectives: To examine primary care physician (PCP) contributions toward racial and sex differences in the diagnosis and treatment of late‐life depression.

Design: Survey using a computerized instrument incorporating video interviews and text, with volunteer PCPs randomly assigned to one of four standardized video vignettes of an elderly patient depicting late‐life depression. Vignettes differed only in the patient/actor's race (white/African‐American) or sex.

Setting: American Academy of Family Physicians meeting, San Diego, California, 2002.

Participants: One hundred seventy‐eight U.S.‐practicing postresidency PCPs who were asked to participate in a clinical decision‐making study.

Measurements: The computerized survey instrument assessed PCPs' diagnoses, first‐line treatment and management recommendations, and judgment of personal characteristics/behaviors for the patients in the vignettes.

Results: Eighty‐five percent of all PCPs correctly diagnosed the elderly patient(s) with major depression. There were no significant differences in the diagnosis of depression, treatment recommendations, or PCP assessment of most patient characteristics by the race or sex of the patient/actor in the vignette, but PCP characteristics, most notably the location of medical school training (U.S. vs international), affected the likelihood of a depression diagnosis and treatment recommendations.

Conclusion: Given standardized symptom‐pictures, PCPs are just as likely to diagnose and treat depression in African‐American as in white older people, suggesting that bias based simply on apparent patient race is not a likely explanation for the lower rates of depression diagnosis and treatment in older African Americans. PCPs who have trained at international medical schools may benefit from targeted training initiatives on the diagnosis and treatment of late‐life depression.
Effects of Behavioral and Drug Therapy on Nocturia in Older Incontinent Women
Authors: Johnson Theodore M. , Burgio Kathryn L. , Redden David T. , Wright Kate Clark , Goode Patricia S.
Published: May 2005

Objectives: To examine changes in nocturia from a multicomponent behavioral training program or drug therapy in older women with urge or mixed (urge‐predominant) urinary incontinence.

Design: A secondary analysis of data from a prospective, randomized clinical trial.

Setting: Parent trial was an outpatient research protocol in Alabama.

Participants: One hundred ninety‐seven women (aged 55–92) with incontinence and urodynamic evidence of bladder dysfunction. At baseline, 131 women (66% of participants) had nocturia.

Intervention: In the parent study, participants received behavioral training, including four sessions of biofeedback‐assisted pelvic floor muscle exercises, drug treatment (oxybutynin IR titrated from 2.5 mg per day to 5.0 mg three times a day), or placebo.

Measurements: Participant‐completed bladder diaries were used to calculate changes in nocturia.

Results: Behavioral training reduced nocturia by a median 0.50 episodes per night and was significantly more effective than drug treatment (median reduction=0.30 episodes; P=.02) and placebo (median reduction=0.00 episodes; P<.001). Also, drug treatment was more effective than control (P=.007).

Conclusion: Both behavioral training and drug treatment reduced nocturia more than placebo, but behavioral training was the most effective.
Community‐Acquired Pneumonia in Patients Receiving Home Care
Authors: Marrie Thomas J. , Huang Jane Q.
Published: May 2005

Objectives: To describe the features of community‐acquired pneumonia (CAP) requiring hospitalization in subjects receiving home care.

Design: Prospective study from November 15, 2000, to November 14, 2002.

Setting: Six hospitals in the Edmonton, Canada, area.

Participants: Two thousand four hundred sixty‐four subjects aged 17 years and older with CAP, 21.9% of whom were receiving home care.

Measurements: Pneumonia attack rates, demographic features, severity of illness, medication, length of stay, mortality, in hospital complications, and time to achieve physiological stability.

Results: The overall rate of CAP requiring a visit to an emergency department in home care recipients was 25 per 1,000 person years, 90.8% of whom were admitted to the hospital for treatment. Patients who were receiving home care at the time of admission were older and less likely to be current tobacco smokers, had higher in‐hospital mortality (11%) and a longer length of stay, were receiving more medications, and had more comorbidity and fewer symptoms except for shortness of breath and altered mental state than those who were not receiving home care. Home care patients had four times as many myocardial infarctions and recurrent aspiration as the non‐home care patients. Falls occurred five times more often, and urinary catheters were inserted twice as often. Except for oxygen saturation, time to achieve physiological stability was the same for the two groups of patients. Half (51.2%) of the home care patients passed the get‐up‐and‐go test, compared with 75% (P<.001) of the non‐home care patients.

Conclusion: Home care patients with CAP had an 11% mortality rate and a higher rate of complications than those who did not receive home care.
Use of Serial Mini‐Mental State Examinations to Diagnose and Monitor Delirium in Elderly Hospital Patients
Authors: O'Keeffe Shaun T. , Mulkerrin Eamon C. , Nayeem Kayser , Varughese Matthew , Pillay Isweri
Published: May 2005

Objectives: To determine the responsiveness of serial Mini‐Mental State Examinations (MMSEs) for the diagnosis and monitoring of delirium in elderly hospital patients.

Design: Prospective study.

Setting: University teaching hospital.

Participants: One hundred sixty‐five people admitted to an acute geriatric service.

Measurements: Subjects were assessed using the MMSE and the Confusion Assessment Method on hospital Days 1 and 6. Changes in scores were compared between patients who remained free of delirium (n=124) and those who by Day 6 had developed delirium (n=14) or had resolution of delirium present on admission (n=22).

Results: A number of measures of responsiveness confirmed that serial MMSE scores were responsive to resolution and to development of delirium. A fall of 2 or more points on the MMSE was the best determinant for detecting development of delirium (93% sensitivity, 90% specificity, positive likelihood ratio (LR)=8.9 (95% confidence interval (CI)=5.2–15.1) and negative LR=0.08 95% CI=0.01–0.53)). A rise of 3 or more points was the best determinant for detecting resolution of delirium (77% sensitivity, 75% specificity, positive LR=3.1 (95% CI=2.1–4.5) and negative LR=0.30 (95% CI=0.14–0.66)).

Conclusion: The MMSE is responsive to short‐term changes in cognitive function in elderly patients. Serial MMSE tests should be helpful in monitoring the development and resolution of delirium in this population.
Perceived Barriers to Trying Self‐Management Approaches for Chronic Pain in Older Persons
Authors: Austrian Jonathan S. , Kerns Robert D. , Carrington Reid M.
Published: May 2005

Objectives: To examine older persons' willingness to participate in exercise and relaxation programs for managing chronic pain, to identify characteristics associated with willingness to participate, and to ascertain their barriers to participation.

Design: Cross‐sectional survey.

Setting:

A geriatric ambulatory care practice located in New York, New York, and the General Clinical Research Center of Weill Cornell Medical College.

Participants: Sixty‐eight English‐speaking patients aged 70 and older with chronic pain.

Measurements: Participants' level of willingness to participate in the programs was assessed using 5‐point Likert scales, and information regarding their demographic, clinical, psychological, and pain status was obtained. Qualitative methods were used to ascertain participants' perceived barriers to participation.

Results: Participants had a mean age±standard deviation of 81.9±7.0 and were mostly white (85%) and female (68%). Although only 16% of participants reported current use of exercise as a pain‐management strategy, 73% reported a willingness to try the exercise program. Four percent reported current use of relaxation methods; 70% reported an interest in learning these techniques. Moderate correlations were found between increasing days of restricted activity due to pain and greater willingness to participate. Seventeen unique barriers were identified; the mean number of barriers reported per person was 2.9±1.8 for exercise and 2.2±1.4 for relaxation. Commonly reported barriers to participating in either program included time conflicts, transportation, treatment efficacy concerns, and fear of pain or injury.

Conclusion: Older primary care patients with chronic pain are willing to try exercise and relaxation therapies to help manage pain but report a substantial number of barriers to participating in these programs. Addressing patient‐level barriers could improve engagement in and adherence to exercise and relaxation therapies for managing pain in older persons.
Simplifying Detection of Cognitive Impairment: Comparison of the Mini‐Cog and Mini‐Mental State Examination in a Multiethnic Sample
Authors: Borson Soo , Scanlan James M. , Watanabe Jill , Tu Shin‐Ping , Lessig Mary
Published: May 2005

Objectives: To compare detection of cognitive impairment using the Mini‐Cog and Mini‐Mental State Examination (MMSE) and to identify sociodemographic variables that influence detection in an ethnoculturally diverse sample.

Design: Cross‐sectional.

Setting: A registry of the University of Washington Alzheimer's Disease Research Center Satellite.

Participants: A heterogeneous community sample (n=371) of predominantly ethnic minority elderly assessed using a standardized research protocol, 231 of whom met criteria for dementia or mild cognitive impairment (MCI).

Measurements: Demographic data, a standardized research protocol for cognitive assessment and dementia diagnosis, MMSE, and Mini‐Cog.

Results: Both screens effectively detected cognitive impairment, the Mini‐Cog slightly better than the MMSE (P<.01). Overall accuracy of classification was 83% for the Mini‐Cog and 81% for the MMSE. The Mini‐Cog was superior in recognizing patients with Alzheimer‐type dementias (P=.05). Low education negatively affected detection using the MMSE (P<.001), whereas education did not affect the Mini‐Cog, and low literacy minimally affected it.

Conclusion: The Mini‐Cog detects clinically significant cognitive impairment as well as or better than the MMSE in multiethnic elderly individuals, is easier to administer to non‐English speakers, and is less biased by low education and literacy.
ESAT-6/CFP-10 Fusion Protein and Peptides for Optimal Diagnosis of
Mycobacterium tuberculosis
Infection by Ex Vivo Enzyme-Linked Immunospot Assay in The Gambia
Authors: Hill Philip C. , Jackson-Sillah Dolly , Fox Annette , Franken Kees L. M. C. , Lugos Moses D. , Jeffries David J. , Donkor Simon A. , Hammond Abdulrahman S. , Adegbola Richard A. , Ottenhoff Tom H. M. , Klein Michel R. , Brookes Roger H.
Published: May 2005

Overlapping peptides of
Mycobacterium tuberculosis
antigens ESAT-6 and CFP-10 offer increased specificity over the purified protein derivative skin test when they were used in an ex vivo enzyme-linked immunospot (ELISPOT) assay for gamma interferon detection for the diagnosis of
M. tuberculosis
infection from recent exposure. We assessed whether equivalent results could be obtained for a fusion protein of the two antigens and whether a combined readout would offer increased sensitivity in The Gambia. We studied the ELISPOT assay results for 488 household contacts of 88 sputum smear-positive tuberculosis (TB) cases. The proportions of subjects positive by each test and by the tests combined were assessed across an exposure gradient, defined according to sleeping proximity to a TB case. Eighty-eight (18%) subjects were positive for CFP-10 peptides, 148 (30%) were positive for ESAT-6 peptides, 161 (33%) were positive for both peptides, and 168 (34%) were positive for the fusion protein; 188 (39%) subjects had either a positive result for a peptide or a positive result for the fusion protein. There was reasonable agreement between the peptide and the protein results (kappa statistic = 0.78) and no significant discordance (
P
= 0.38). There was a strong correlation between the fusion protein and combined peptide spot counts (
r
= 0.9), and responses to the peptide and the proteins all increased significantly according to
M. tuberculosis
exposure. The proportion of subjects positive for either the pool of peptides or the fusion protein offered maximum sensitivity, being significantly higher than the proportion of subjects positive for ESAT-6 peptides alone (
P
= 0.007). A fusion protein of ESAT-6 and CFP-10 is equivalent to overlapping peptides for the diagnosis of latent
M. tuberculosis
infection. Use of a combination of peptides and fusion protein offers improved sensitivity.
Use of the Oxford Multilocus Sequence Typing Protocol and Sequencing of the Flagellin Short Variable Region To Characterize Isolates from a Large Outbreak of Waterborne
Campylobacter
sp. Strains in Walkerton, Ontario, Canada
Authors: Clark Clifford G. , Bryden Louis , Cuff Wilfred R. , Johnson Patricia L. , Jamieson Frances , Ciebin Bruce , Wang Gehua
Published: May 2005

The Walkerton (Ontario, Canada) outbreak of waterborne
Escherichia coli
O157:H7 and
Campylobacter jejuni
was quite limited in both space and time, making it a good model for exploring the utility of different typing and subtyping methods for the characterization of relationships among isolates of these organisms. We have extended previous work with these organisms through analysis by the Oxford multilocus sequence typing (MLST) and the flagellin short variable region (fla-SVR) sequencing methods. Additional isolates not epidemiologically related to the Walkerton outbreak have also been included. Both sequencing methods identified and differentiated between Walkerton outbreak strains 1 and 2. When these strains were compared with isolates that were not part of the outbreak, the information produced by the fla-SVR method more often correlated with epidemiological findings than that produced by MLST, though both methods were required for optimal discrimination. The MLST data were more relevant in terms of the overall population structure of the organisms. Both mutation and recombination appeared to be responsible for generating diversity among the isolates tested.
Dissemination of Community-Acquired Methicillin-Resistant
Staphylococcus aureus
Clones in Northern Norway: Sequence Types 8 and 80 Predominate
Authors: Hanssen Anne-Merethe , Fossum Aina , Mikalsen Jarle , Halvorsen Dag S. , Bukholm Geir , Sollid Johanna U. Ericson
Published: May 2005

Increasing frequencies of community-acquired methicillin-resistant
Staphylcoccus aureus
(MRSA) strain isolation have been reported from many countries. The overall prevalence of MRSA in Norway is still very low. MRSA isolates (
n
= 67) detected between 1995 and 2003 in northern Norway were analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, and staphylococcal cassette chromosome
mec
(SCC
mec
) typing. Sixty-seven isolates were associated with 13 different sequence types. Two successful MRSA clones predominated. Sequence type 8 (ST8) (40%) and ST80 (19%) containing SCC
mec
type IV were detected in hospitals and communities in different geographic regions during a 7-year period. In general, there was a low level of antimicrobial resistance. Only 26% of the isolates were multiresistant. International epidemic clones were detected. The frequent findings of SCC
mec
type IV (91%) along with heterogeneous genetic backgrounds suggest a horizontal spread of SCC
mec
type IV among staphylococcal strains in parallel with the clonal spread of successful MRSA strains.
Evaluation of the COBAS Hepatitis C Virus (HCV) TaqMan Analyte-Specific Reagent Assay and Comparison to the COBAS Amplicor HCV Monitor V2.0 and Versant HCV bDNA 3.0 Assays
Authors: Konnick Eric Q. , Williams Sheri M. , Ashwood Edward R. , Hillyard David R.
Published: May 2005

Performance characteristics of the COBAS hepatitis C virus (HCV) TaqMan analyte-specific reagent (TM-ASR) assay using the QIAGEN BioRobot 9604 for RNA extraction were evaluated and compared to the COBAS Amplicor HCV Monitor V2.0 (Amplicor) and Versant HCV bDNA 3.0 (Versant) assays using clinical samples. Calibration of TM-ASR using Armored RNA allowed determination of the distribution of HCV RNA in clinical samples, using 22,399 clinical samples. Limit of detection, linearity, and inter- and intraassay assay precision were determined for the TM-ASR assay using multiple clinical specimen panels across multiple determinations. Genotype specificity for the TM-ASR assay was determined using samples with different HCV RNA genotypes evaluated and compared against predetermined results. Contamination control of the TM-ASR assay was evaluated using pools of HCV RNA-positive and -negative samples tested in a checkerboard pattern over 12 runs of 96 samples. Correlation of the TM-ASR, Amplicor, and Versant assays was determined using 100 paired clinical samples and Deming regression analysis. The TM-ASR performed well with respect to linearity, precision, and contamination control. The correlation between TM-ASR and the Amplicor and Versant assays was poor, with large differences between assay results for individual samples. Calibration of the TM-ASR assay with Armored RNA allowed for a wide dynamic range and description of the distribution of HCV RNA in clinical samples.
Targeted Hybridization of IS
6110
Fingerprints Identifies the W-Beijing
Mycobacterium tuberculosis
Strains among Clinical Isolates
Authors: Kurepina Natalia , Likhoshvay Ekaterina , Shashkina Elena , Mathema Barun , Kremer Kristin , van Soolingen Dick , Bifani Pablo , Kreiswirth Barry N.
Published: May 2005

Targeted IS
6110
-based RFLP genotyping can be applied to rapidly identify specific groups of biomedically/epidemiologically relevant
Mycobacterium tuberculosis
clinical isolates. One such group is the W-Beijing strain family (also known as Beijing/W), implicated in significant nosocomial and community outbreaks worldwide. Using previously defined criteria, we developed a simple and accurate method to identify members of the W-Beijing family, based on rehybridization of Southern blot membranes used previously in routine IS
6110
DNA fingerprint analysis. The hybridization probe constructed (“W-Beijing polyprobe”) contains the PCR-amplified fragments specific for three
M. tuberculosis
chromosomal loci used for the identification of W-Beijing strains. The targets include the
dnaA-dnaN
and NTF regions and the direct repeat locus. A total of 526 selected clinical isolates (representative of 253 different IS
6110
-defined strain types) were analyzed using the W-Beijing polyprobe. A total of 148 isolates from this collection were found to be members of the W-Beijing phylogenetic lineage, comprising 106 strains from the W-Beijing family (46 clusters) and 42 related isolates. Rehybridization results were confirmed by computer-assisted analysis. The sensitivity and specificity of this method were estimated at 98.7% and 99.7%, respectively. This study demonstrates that the W-Beijing polyprobe can accurately and reliably discriminate members of the W-Beijing phylogenetic lineage and the W-Beijing family of
M. tuberculosis
strains.
Global Trends in the Antifungal Susceptibility of
Cryptococcus neoformans
(1990 to 2004)
Authors: Pfaller M. A. , Messer S. A. , Boyken L. , Rice C. , Tendolkar S. , Hollis R. J. , Doern G. V. , Diekema D. J.
Published: May 2005

The antifungal susceptibilities of 1,811 clinical isolates of
Cryptococcus neoformans
obtained from 100 laboratories in 5 geographic regions worldwide between 1990 and 2004 were determined. The MICs of amphotericin B, flucytosine, fluconazole, voriconazole, posaconazole, and ravuconazole were determined by the National Committee for Clinical Laboratory Standards broth microdilution method. Isolates were submitted to a central reference laboratory (University of Iowa) from study centers in Africa (5 centers, 395 isolates), Europe (14 centers, 102 isolates), Latin America (14 centers, 82 isolates), the Pacific region (7 centers, 50 isolates), and North America (60 centers, 1,182 isolates). Resistance to amphotericin B, flucytosine, and fluconazole was ≤1% overall. Susceptibility to flucytosine (MIC, ≤4 μg/ml) ranged from 35% in North America to 68% in Latin America. Similarly, only 75% of isolates from North America were susceptible to fluconazole (MIC, ≤8 μg/ml) compared to 94 to 100% in the other regions. Isolates remained highly susceptible to amphotericin B (99% susceptibility at a MIC of ≤1 μg/ml) over the entire 15-year period. Susceptibility to flucytosine (MIC, ≤4 μg/ml) increased from 34% in 1990 to 1994 to 66% in 2000 to 2004. Susceptibility to fluconazole (MIC, ≤8 μg/ml) increased from 72% in 1990 to 1994 to 96% in 2000 to 2004. Voriconazole, posaconazole, and ravuconazole all were very active (99% of isolates susceptible at MIC of ≤1 μg/ml) against this geographically diverse collection of isolates. We conclude that in vitro resistance to antifungal agents used in the treatment of cryptococcosis remains uncommon among isolates of
C. neoformans
from five broad geographic regions and has not increased over a 15-year period.
Significance of Transiently Positive Enzyme-Linked Immunosorbent Assay Results in Detection of
Helicobacter pylori
in Stool Samples from Children
Authors: Haggerty Thomas D. , Perry Sharon , Sanchez Luz , Perez-Perez Guillermo , Parsonnet Julie
Published: May 2005

In young children, the significance of stool samples transiently positive for
Helicobacter pylori
antigen is unknown. As part of a larger prospective study on enteric infections, stool samples were obtained from 323 children at two time points 3 months apart and tested for
H. pylori
antigen using a commercially available enzyme-linked immunosorbent assay (ELISA) test. Seminested PCR for a
Helicobacter
-specific 16S rRNA gene was performed on all 26 pairs reverting from positive to negative (transient positives), all 4 persistent antigen-positive pairs, and 10 randomly selected persistent antigen-negative pairs.
Helicobacter
species were amplified from the first stool samples of 15/26 (58%) of the transient positives and 1 (25%) of 4 persistent positives. No
Helicobacter
species were amplified from the 10 persistent negatives. Among the 15 amplicons from transient-positive stool,
H. pylori
was sequenced and identified from 12 (80%; 95% confidence interval, 52% to 96%) and other
Helicobacter
spp. were identified from three (
Helicobacter canis
,
Helicobacter winghamensis
, and MIT 99-5504). Four of the 15 remained positive by PCR for the second (antigen-negative) stool sample, including all 3 initially identified as non-
H. pylori. Helicobacter bilis
was amplified from the second sample of a persistent positive. Two of eight transient positives from whom serum was available had accompanying transient elevations in anti-
H. pylori
antibodies. Transiently positive stool ELISAs for
H. pylori
are common and represent
H. pylori
in the majority of cases where sequences can be obtained. A not-insignificant percentage of antigen-positive stools, however, may represent other
Helicobacter
species.
Genotypic Analysis of the Earliest Known Prehistoric Case of Tuberculosis in Britain
Authors: Taylor G. Michael , Young Douglas B. , Mays Simon A.
Published: May 2005

The earliest known case of human tuberculosis in Britain dates to the middle period of the Iron Age, approximately 2,200 years before present. Bone lesions on the spine of a male skeleton excavated at Tarrant Hinton in Dorset, United Kingdom, show evidence of Pott's disease and are supported by molecular evidence of
Mycobacterium tuberculosis
complex DNA amplified by IS
6110
PCR (19). In the present study, we used a further series of sensitive PCR methods to confirm the diagnosis of tuberculosis and to determine the genotype of the infecting strain. These tests demonstrated that this individual was infected with a strain of
M. tuberculosis
rather than
Mycobacterium bovis
. The strain had undergone the tuberculosis D1 deletion affecting the
mmpS6
and
mmpL6
genes and can therefore be identified as a member of the family of “modern”
M. tuberculosis
isolates. All evidence obtained was consistent with surviving mycobacterial DNA being highly fragmented in this case.
Identification of Non-
Helicobacter pylori
Spiral Organisms in Gastric Samples from Humans, Dogs, and Cats
Authors: Van den Bulck Kathleen , Decostere Annemie , Baele Margo , Driessen Ann , Debongnie Jean-Claude , Burette Alain , Stolte Manfred , Ducatelle Richard , Haesebrouck Freddy
Published: May 2005

Tightly coiled bacteria are a rare cause of gastric pathology in humans and represent a mixture of species for which a zoonotic origin is suspected. Similar organisms are common inhabitants of the gastric mucosae of carnivores and pigs. It was the goal of the present study to determine the actual occurrence of each individual
Helicobacter
species in human, canine, and feline stomachs in order to better understand the possible zoonotic significance. Gastric biopsy samples from humans with histological evidence of non-
Helicobacter pylori
spiral bacteria (
n
= 123) and samples from the gastric antrum, corpus, and cardia from dogs (
n
= 110) and cats (
n
= 43) were subjected to a multiplex PCR, enabling the identification of
Helicobacter felis
,
Helicobacter bizzozeronii
,
Helicobacter salomonis
, and “
Candidatus
Helicobacter suis.” A PCR for detecting
H. pylori
was applied to all human samples. Single infections with “
Candidatus
Helicobacter suis,”
H. felis
,
H. bizzozeronii
,
H. salomonis
, a hitherto unknown genotype of a non-
H. pylori
spiral organism (
Helicobacter
-like organism 135 [HLO135]), and
H. pylori
were identified in 30.9%, 8.9%, 2.4%, 11.4%, 7.3%, and 8.9% of the human biopsy samples, respectively. Mixed infections (16.3%) with two or even three of these were also found. In the canine stomach,
H. bizzozeronii
(70.0%) was encountered as the main spiral organism, while
H. felis
(62.7%) and HLO135 (67.4%) were the predominant
Helicobacter
species found in the feline gastric mucosa. Although the majority of human non-
H. pylori
organisms are
Helicobacter
species naturally occurring in the stomachs of pigs, cats, and dogs, the frequent identification of
H. salomonis
in human gastric biopsy samples is in contrast to its rare identification in pet carnivore samples, urging us to suspect other sources of infection.
Genetic and Antigenic Variability of Human Respiratory Syncytial Virus (Groups A and B) Isolated over Seven Consecutive Seasons in Argentina (1995 to 2001)
Authors: Galiano Monica C. , Palomo Concepcion , Videla Cristina M. , Arbiza Juan , Melero José A. , Carballal Guadalupe
Published: May 2005

The genetic and antigenic variability of human respiratory syncytial virus (HRSV) strains isolated in Buenos Aires from 1995 to 2001 was evaluated by partial nucleotide sequencing of the G gene and enzyme-linked immunosorbent assay analysis with anti-G monoclonal antibodies. Phylogenetic analyses showed that 37 group A strains clustered into five genotypes, whereas 20 group B strains clustered into three genotypes. Group A showed more genetic variability than group B. A close correlation between genotypes and antigenic patterns was observed. Changes detected in the G protein of viruses from both groups included (i) amino acid substitutions and(ii) differences in protein length due to either changes in stop codon usage or sequence duplications. Three B strains from 1999 exhibited a duplication of 20 amino acids, while one B strain from 2001 had 2 amino acids duplicated. The comparison among Argentinean HRSV strains and viruses isolated in other geographical areas during different epidemics is discussed.
Molecular Characterization of Vancomycin-Resistant
Enterococcus faecium
Isolates from Korea
Authors: Ko Kwan Soo , Baek Jin Yang , Lee Ji-Young , Oh Won Sup , Peck Kyong Ran , Lee NamYong , Lee Wee Gyo , Lee Kyungwon , Song Jae-Hoon
Published: May 2005

A total of 98 vancomycin-resistant
Enterococcus faecium
(VREF) isolates from four tertiary-care hospitals in Korea during the period between 1998 and 2004 were analyzed for genotypic characteristics using the multiplex PCR, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and
esp
gene analysis. Ninety-two isolates of VREF with VanA phenotype and five of six isolates with VanB phenotype possessed the
vanA
gene. MLST analysis revealed 9 sequence types (STs), which belonged to a single clonal complex (CC78, clonal lineage C1). Five strains showing incongruence between phenotype and genotype (VanB-
vanA
) did not belong to the same genotypic clone. The
esp
gene was detected in all VREF strains, showing 12 different
esp
repeat profiles. Data suggest that an epidemic clonal group of VREF, CC78 with
esp
gene, is also present in Asia and has differentiated into multiple diverse genotypic clones during the evolutionary process.