bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of
Neisseria meningitidis
Isolates from Recent Outbreaks in Ethiopia and Comparison with Those Recovered during the Epidemic of 1988 to 1989
Authors: Norheim Gunnstein , Rosenqvist Einar , Aseffa Abraham , Yassin Mohammed Ahmed , Mengistu Getahun , Kassu Afework , Fikremariam Dereje , Tamire Wegene , Høiby E. Arne , Alebel Tsegaye , Berhanu Degu , Merid Yarid , Harboe Morten , Caugant Dominique A. 
Published: March 2006

ABSTRACT

The objectives of this study were to collect and characterize epidemic meningococcal isolates from Ethiopia from 2002 to 2003 and to compare them to 21 strains recovered during the previous large epidemic of 1988 to 1989. Ninety-five patients in all age groups with clinical signs of meningitis and a turbid cerebrospinal fluid (CSF) sample were included in the study of isolates from 2002 to 2003. Seventy-one patients (74.7%) were confirmed as having
Neisseria meningitidis
either by culture (
n
= 40) or by
porA
PCR (
n
= 31) of their CSF. The overall case fatality rate (CFR) was 11.6%; the
N. meningitidis
-specific CFR was 4.2%. All 40 strains were fully susceptible to all antibiotics tested except sulfonamide, were serotyped as A:4/21:P1.20,9, and belonged to sequence type 7 (ST-7). The strains from 1988 to 1989 were also equally susceptible and were characterized as A:4/21:P1.20,9, but they belonged to ST-5. Antigenic characterization of the strains revealed differences in the repertoire of lipooligosaccharides and Opa proteins between the old and the recent strains. PCR analysis of the nine
lgt
genes revealed the presence of the
lgtAHFG
genes in both old and recent strains;
lgtB
was present in only some of the strains, but no correlation with sequence type was observed. Further analysis showed that in addition to their
pgm
alleles, the Ethiopian ST-5 and ST-7 strains also differed in their
tbpB
,
opa
,
fetA
, and
lgtA
genes. The occurrence of new antigenic structures in strains sharing the same serogroup, PorA, and PorB may help explain the replacement of ST-5 by ST-7 in the African meningitis belt.
Differentiating Host-Associated Variants ofMycobacterium aviumby PCR for Detection of Large Sequence Polymorphisms
Authors: Semret Makeda , Turenne Christine Y. , de Haas Petra , Collins Desmond M. , Behr Marcel A. 
Published: March 2006

ABSTRACTTheMycobacterium aviumspecies consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-typeM. aviumisolates and from cattle types and sheep types ofM. aviumsubsp.paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly typeM. aviumisolates into these subgroups.
Detection and Genotyping of SHV β-Lactamase Variants by Mass Spectrometry after Base-Specific Cleavage of In Vitro-Generated RNA Transcripts
Authors: Stürenburg Enno , Storm Niels , Sobottka Ingo , Horstkotte Matthias A. , Scherpe Stefanie , Aepfelbacher Martin , Müller Susanne 
Published: March 2006

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR-amplified and in vitro-transcribed
bla
SHV
genes was used for the identification and genotyping of SHV β-lactamases. For evaluation,
bla
SHV
stretches of 21 clinical
Enterobacteriaceae
isolates were PCR amplified using T7 promoter-tagged forward and reverse primers, respectively. In vitro transcripts were generated with T7 RNA and DNA polymerase in the presence of modified analogues replacing either CTP or UTP. Using RNase A, the in vitro transcripts were base-specifically cleaved at every “T” or “C” position. Resulting cleavage products were analyzed by MALDI-TOF MS, generating a characteristic signal pattern based on the fragment masses. All 21 individual SHV genes were identified unambiguously using reference sequences, and the results were in perfect concordance with those obtained by fluorescent dideoxy sequencing, which represents the current standard method. As multiple point mutations can be detected in a single assay and newly emerged mutations which are not yet described in public databases can be identified too, MALDI-TOF MS appears to be an ideal tool for analysis of sequence polymorphisms in resistance-associated gene loci.
Comparison of Culture and a Novel 5′
Taq
Nuclease Assay for Direct Detection of
Campylobacter fetus
subsp.
venerealis
in Clinical Specimens from Cattle
Authors: McMillen Lyle , Fordyce Geoffry , Doogan Vivienne J. , Lew Ala E. 
Published: March 2006

ABSTRACT

A
Campylobacter fetus
subsp.
venerealis
-specific 5′
Taq
nuclease PCR assay using a 3′ minor groove binder-DNA probe (TaqMan MGB) was developed based on a subspecies-specific fragment of unknown identity (S. Hum, K. Quinn, J. Brunner, and S. L. On, Aust. Vet. J. 75:827-831, 1997). The assay specifically detected four
C. fetus
subsp.
venerealis
strains with no observed cross-reaction with
C. fetus
subsp.
fetus
-related
Campylobacter
species or other bovine venereal microflora. The 5′
Taq
nuclease assay detected approximately one single cell compared to 100 and 10 cells in the conventional PCR assay and 2,500 and 25,000 cells from selective culture from inoculated smegma and mucus, respectively. The respective detection limits following the enrichments from smegma and mucus were 5,000 and 50 cells/inoculum for the conventional PCR compared to 500 and 50 cells/inoculum for the 5′
Taq
nuclease assay. Field sampling confirmed the sensitivity and the specificity of the 5′
Taq
nuclease assay by detecting an additional 40 bulls that were not detected by culture. Urine-inoculated samples demonstrated comparable detection of
C. fetus
subsp.
venerealis
by both culture and the 5′
Taq
nuclease assay; however, urine was found to be less effective than smegma for bull sampling. Three infected bulls were tested repetitively to compare sampling tools, and the bull rasper proved to be the most suitable, as evidenced by the improved ease of specimen collection and the consistent detection of higher levels of
C. fetus
subsp.
venerealis
. The 5′
Taq
nuclease assay demonstrates a statistically significant association with culture (χ
2
= 29.8;
P
< 0.001) and significant improvements for the detection of
C. fetus
subsp.
venerealis
-infected animals from crude clinical extracts following prolonged transport.
Acute hepatitis B in the era of immunisation: pitfalls in the identification of high risk patients
Authors: Rosner G , Lurie Y , Blendis L , Halpern Z , Oren R 
Published: March 2006

Abstract

Background
Since the adoption of a universal hepatitis B immunisation strategy, the reported incidence of acute hepatitis B has declined dramatically worldwide including in Israel. However, new cases of acute hepatitis B still occur. The aim of this study was to describe the incidence of acute hepatitis B in a referral area, routes of transmission, and outcome.

Methods
The charts of all new hepatitis B patients, who visited the clinic in the years 2002 and 2003 (January 2002 to December 2003), were reviewed. The main criteria for a diagnosis of acute hepatitis B were transient increase of alanine transaminase activity, and hepatitis B surface antigen seroconversion.

Results
Twenty nine men and seven women were diagnosed with acute hepatitis B infection during the study period. Two patients were previously vaccinated with hepatitis B vaccine. One case of hepatitis D coinfection was reported. The incidence of acute hepatitis B in the referral area was estimated as 2.25 per 100 000 adult population. Mean age was 36 years (17–75). Twenty one patients (18 men and 3 women) acquired the virus through unprotected sexual contact, and seven patients through iatrogenic exposure. Thirty three patients underwent spontaneous seroconversion while three patients became chronic carriers.

Conclusions
Despite a universal immunisation policy, frequent cases of acute hepatitis B in Israel are still seen. High risk heterosexual activity and iatrogenic exposure seem to be the commonest routes of transmission. Further recommendations regarding vaccination policy are discussed.
Ageing and the auditory system
Authors: Howarth A , Shone G R 
Published: March 2006

Abstract
There are a number of pathophysiological processes underlying age related changes in the auditory system. The effects of hearing loss can have consequences beyond the immediate loss of hearing, and may have profound effects on the functioning of the person. While a deficit in hearing can be corrected to some degree by a hearing aid, auditory rehabilitation requires much more than simply amplifying external sound. It is important that those dealing with elderly people are aware of all the issues involved in age related hearing loss.
Is non-steroidal anti-inflammaory drug (NSAID) enteropathy clinically more important than NSAID gastropathy?
Authors: Adebayo D , Bjarnason I 
Published: March 2006

Abstract
The side effects of conventional non-steroidal anti-inflammatory drugs (NSAIDs) on the stomach is undoubtedly a serious public health problem contributing significantly to the morbidity and mortality of patients receiving these drugs. However, the damage of NSAIDs is not confined to the stomach. Indeed the short term and long term damage of NSAIDs on the small bowel (NSAID enteropathy) is more frequent than NSAID gastropathy. Furthermore, NSAID enteropathy is associated with complications (bleeding and protein loss). While many of these are mild, the serious events (significant bleeding, perforation, obstruction, and sudden death) are frequent as that reported for NSAID gastropathy. The diagnosis of NSAID enteropathy has been greatly aided by the introduction of wireless capsule enteroscopy.
Exploratory Study of Some Acoustic and Articulatory Characteristics of Sad Speech
Authors: Erickson Donna , Yoshida Kenji , Menezes Caroline , Fujino Akinori , Mochida Takemi , Shibuya Yoshiho 
Published: March 2006

AbstractThis study examines acoustic and articulatory EMA data of two female speakers(American and Japanese) spontaneously producing emotional speech whileengaged in an informal telephone-type conversation. A set of control data inwhich the speakers imitated or read the original emotional utterance was alsorecorded; for the American speaker, the intonation pattern was also imitated. Theresults suggest (1) acoustic and articulatory characteristics of spontaneous sadspeech differ from that of read speech or imitated intonation speech, (2) spontaneoussad speech and imitated sad speech seem to have similar acoustic characteristics(high F0, changed F1 as well as voice quality), but articulation is different interms of lip, jaw and tongue positions, and (3) speech that is rated highly by listenersas sad is associated with high F0 and changed voice quality.
Predicting Mortality in Spontaneous Intracerebral Hemorrhage
Authors: Godoy Daniel Agustin , Piñero Gustavo , Di Napoli Mario 
Published: March 2006

Background and Purpose—A clinical grading scale for intracerebral hemorrhage (ICH), formally ICH score, was recently developed showing to predict 30-day mortality in a simple and reliable manner. The aim of the present study was to validate the original ICH (oICH) score in an independent cohort of patients from a developing country assessing 30-day mortality and 6-month functional outcome and whether its modifications can improve prediction.Methods—Consecutive patients admitted with acute ICH between January 1, 2003, and July 31, 2004, were prospectively included. oICH score was applied and 2 modified ICH (mICH) scores were created with the same variables, except localization, of the oICH score but with different cutoff values. Outcome was assessed as 30-day mortality and 6-month good outcome (Glasgow Outcome Scale [GOS] 4 to 5).Results—A total of 153 patients were included during study period. Thirty-day mortality rate was 34.6% (n=53), and 59 patients (38.6%) had good functional outcome (GOS 4 to 5) at 6 months. The oICH and mICH scores predicted mortality equally well. According to Youden’s index (J), the oICH score was a reliable predictor for mortality (J=0.59) but less reliable for predicting good outcome (J=0.54). The mICH scores were equal in predicting mortality but better for predicting good outcome than the oICH score (J=0.60).Conclusions—oICH score also confirms its validity in a socially and culturally different population. Modifications of oICH do not improve its 30-day mortality prediction but improve its ability to predict good functional outcome at 6 months.
Impact of Great Salinity Anomalies on the Low-Frequency Variability of the North Atlantic Climate
Authors: Zhang Rong , Vallis Geoffrey K. 
Published: March 2006

Abstract
In this paper, it is shown that coherent large-scale low-frequency variabilities in the North Atlantic Ocean—that is, the variations of thermohaline circulation, deep western boundary current, northern recirculation gyre, and Gulf Stream path—are associated with high-latitude oceanic Great Salinity Anomaly events. In particular, a dipolar sea surface temperature anomaly (warming off the U.S. east coast and cooling south of Greenland) can be triggered by the Great Salinity Anomaly events several years in advance, thus providing a degree of long-term predictability to the system. Diagnosed phase relationships among an observed proxy for Great Salinity Anomaly events, the Labrador Sea sea surface temperature anomaly, and the North Atlantic Oscillation are also discussed.
Increased Occurrence of Stratospheric Sudden Warmings during El Niño as Simulated by WACCM
Authors: Taguchi Masakazu , Hartmann Dennis L. 
Published: March 2006

Abstract
Experiments with Whole Atmosphere Community Climate Model (WACCM) under perpetual January conditions indicate that stratospheric sudden warmings (SSWs) are twice as likely to occur in El Niño winters than in La Niña winters, in basic agreement with the limited observational dataset. Tropical SST anomalies that mimic El Niño and La Niña lead to changes in the shape of probability distribution functions (PDFs) of stratospheric day-to-day variability, resulting in a warmer pole and weaker vortex on average for El Niño conditions. The tropical SST forcing induces a response similar to the observed response in the enhancement of the planetary wave of zonal wavenumber 1 (wave 1) and the weakening of wave 2 in the upper troposphere and stratosphere of high latitudes. The enhanced wave 1 contributes to a shift of the PDFs of poleward eddy heat flux in the lower stratosphere, or wave forcing entering the stratosphere. The shift of the PDFs includes an increase of strong wave events that induce more frequent SSWs.
E-selectin permits communication between PAF receptors and TRPC channels in human neutrophils
Authors: McMeekin Sarah R. , Dransfield Ian , Rossi Adriano G. , Haslett Christopher , Walker Trevor R. 
Published: March 2006

AbstractThe selectin family of molecules (L-, P-, and E-selectin) mediates adhesive interactions between leukocytes and endothelial cells required for recruitment of leukocytes to inflammatory sites. Soluble E-selectin levels are elevated in inflammatory diseases and act to promote neutrophil β2-integrin–mediated adhesion by prolonging Ca2+ mobilization. Although soluble E-selectin alone was unable to initiate Ca2+ signaling, it allowed a novel “permissive” store-operative calcium entry (SOCE) following the initial platelet-activating factor (PAF)–induced release of Ca2+ from inositol 1,4,5-trisphosphate (IP3)–sensitive stores. This induction of permissive SOCE in response to soluble E-selectin and PAF was shown to act through a G protein-coupled receptor (GPCR) coupled to pertussis toxin-insensitive Gq/11. Furthermore, we demonstrated that permissive SOCE was mediated by canonical transient receptor potential channel (TRPC) due to its sensitivity to specific inhibition by MRS1845 and Gd3+ and that TRPC6 was the principal TRPC family member expressed by human neutrophils. In terms of mechanism, we demonstrated that soluble E-selectin activated Src family tyrosine kinases, an effect that was upstream of phosphatidylinositol 3′-kinase in a signaling pathway that regulates permissive SOCE following exposure of neutrophils to PAF. In summary, this report provides the first evidence for communication between an inflammatory mediator and adhesion receptors at a molecular level, through selectin receptor ligation allowing permissive SOCE to occur following PAF stimulation of human neutrophils.
GONOME: measuring correlations between GO terms and genomic positions
Authors: Stanley Stefan M , Bailey Timothy L , Mattick John S 
Published: February 2006

Abstract

Background:
Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions.

Results:
We present an algorithm – GONOME – that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least) the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For example, we show that, when gene length is taken into account, the term "development" is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE) upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'.

Conclusion:
GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes. Inappropriate use of existing algorithms that do not take gene size into account has led to erroneous or suspect conclusions. Reciprocally GONOME may be used to identify new features in genomes that are significantly associated with particular categories of genes.
Patient and health care system delays in the start of tuberculosis treatment in Norway
Authors: Farah Mohamed Guled , Rygh Jens Henning , Steen Tore W , Selmer Randi , Heldal Einar , Bjune Gunnar 
Published: February 2006

Abstract

Background
Delay in start of tuberculosis (TB) treatment has an impact at both the individual level, by increasing the risk of morbidity and mortality, and at the community level, by increasing the risk of transmission. The aims of this study were to assess the delays in the start of treatment for TB patients in Oslo/Akershus region, Norway and to analyze risk factors for the delays.

Methods
This study was based on information from the National TB Registry, clinical case notes from hospitals and referral case notes from primary health care providers. Delays were divided into patient, health care system and total delays. The association with sex, birthplace, site of the disease and age group was analyzed by multiple linear regression.

Results
Among the 83 TB patients included in this study, 71 (86%) were born abroad. The median patient, health care system and total delays were 28, 33 and 63 days respectively, with a range of 1–434 days. In unadjusted analysis, patient delay and health care system delay did not vary significantly between men and women, according to birthplace or age group. Patients with extra-pulmonary TB had a significantly longer patient, health care system and total delay compared to patients with pulmonary TB. Median total delay was 81 and 56 days in the two groups of TB patients respectively. The health care system delay exceeded the patient delay for those born in Norway. The age group 60+ years had significantly shorter patient delay than the reference group aged 15–29 years when adjusted for multiple covariates. Also, in the multivariate analysis patients born in Norway had significantly longer health care system delay than patients born abroad.

Conclusion
A high proportion of patients had total delays in start of TB treatment exceeding two months. This study emphasizes the need of awareness of TB in the general population and among health personnel. Extra-pulmonary TB should be considered as a differential diagnosis in unresolved cases, especially for immigrants from high TB prevalence countries.
An ultra-low-power image compressor for capsule endoscope
Authors: Lin Meng-Chun , Dung Lan-Rong , Weng Ping-Kuo 
Published: February 2006

Abstract

Background
Gastrointestinal (GI) endoscopy has been popularly applied for the diagnosis of diseases of the alimentary canal including Crohn's Disease, Celiac disease and other malabsorption disorders, benign and malignant tumors of the small intestine, vascular disorders and medication related small bowel injury. The wireless capsule endoscope has been successfully utilized to diagnose diseases of the small intestine and alleviate the discomfort and pain of patients. However, the resolution of demosaicked image is still low, and some interesting spots may be unintentionally omitted. Especially, the images will be severely distorted when physicians zoom images in for detailed diagnosis. Increasing resolution may cause significant power consumption in RF transmitter; hence, image compression is necessary for saving the power dissipation of RF transmitter. To overcome this drawback, we have been developing a new capsule endoscope, called GICam.

Methods
We developed an ultra-low-power image compression processor for capsule endoscope or swallowable imaging capsules. In applications of capsule endoscopy, it is imperative to consider battery life/performance trade-offs. Applying state-of-the-art video compression techniques may significantly reduce the image bit rate by their high compression ratio, but they all require intensive computation and consume much battery power. There are many fast compression algorithms for reducing computation load; however, they may result in distortion of the original image, which is not good for use in the medical care. Thus, this paper will first simplify traditional video compression algorithms and propose a scalable compression architecture.

Conclusion
As the result, the developed video compressor only costs 31 K gates at 2 frames per second, consumes 14.92 mW, and reduces the video size by 75% at least.