bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vorticity structure and evolution in a transverse jet
Authors: MARZOUK YOUSSEF M. , GHONIEM AHMED F. 
Published: March 2007

Transverse jets arise in many applications, including propulsion, effluent dispersion, oil field flows, and V/STOL aerodynamics. This study seeks a fundamental, mechanistic understanding of the structure and evolution of vorticity in the transverse jet. We develop a high-resolution three-dimensional vortex simulation of the transverse jet at large Reynolds number and consider jet-to-crossflow velocity ratiosrranging from 5 to 10. A new formulation of vorticity-flux boundary conditions accounts for the interaction of channel wall vorticity with the jet flow immediately around the orifice. We demonstrate that the nascent jet shear layer contains not only azimuthal vorticity generated in the jet pipe, but wall-normal and azimuthal perturbations resulting from the jet–crossflow interaction. This formulation also yields analytical expressions for vortex lines in the near field as a function ofr.Transformation of the cylindrical shear layer emanating from the orifice begins with axial elongation of its lee side to form sections of counter-rotating vorticity aligned with the jet trajectory. Periodic roll-up of the shear layer accompanies this deformation, creating complementary vortex arcs on the lee and windward sides of the jet. Counter-rotating vorticity then drives lee-side roll-ups in the windward direction, along the normal to the jet trajectory. Azimuthal vortex arcs of alternating sign thus approach each other on the windward boundary of the jet. Accordingly, initially planar material rings on the shear layer fold completely and assume an interlocking structure that persists for several diameters above the jet exit. Though the near field of the jet is dominated by deformation and periodic roll-up of the shear layer, the resulting counter-rotating vorticity is a pronounced feature of the mean field; in turn, the mean counter-rotation exerts a substantial influence on the deformation of the shear layer. Following the pronounced bending of the trajectory into the crossflow, we observe a sudden breakdown of near-field vortical structures into a dense distribution of smaller scales. Spatial filtering of this region reveals the persistence of counter-rotating streamwise vorticity initiated in the near field.
Comparative annotation of viral genomes with non-conserved gene structure
Authors: de Groot Saskia , Mailund Thomas , Hein Jotun 
Published: March 2007

AbstractMotivation: Detecting genes in viral genomes is a complex task. Due to the biological necessity of them being constrained in length, RNA viruses in particular tend to code in overlapping reading frames. Since one amino acid is encoded by a triplet of nucleic acids, up to three genes may be coded for simultaneously in one direction. Conventional hidden Markov model (HMM)-based gene-finding algorithms may typically find it difficult to identify multiple coding regions, since in general their topologies do not allow for the presence of overlapping or nested genes. Comparative methods have therefore been restricted to likelihood ratio tests on potential regions as to being double or single coding, using the fact that the constrictions forced upon multiple-coding nucleotides will result in atypical sequence evolution. Exploiting these same constraints, we present an HMM based gene-finding program, which allows for coding in unidirectional nested and overlapping reading frames, to annotate two homologous aligned viral genomes. Our method does not insist on conserved gene structure between the two sequences, thus making it applicable for the pairwise comparison of more distantly related sequences.Results: We apply our method to 15 pairwise alignments of six different HIV2 genomes. Given sufficient evolutionary distance between the two sequences, we achieve sensitivity of ∼84–89% and specificity of ∼97–99.9%. We additionally annotate three pairwise alignments of the more distantly related HIV1 and HIV2, as well as of two different hepatitis viruses, attaining results of ∼87% sensitivity and ∼98.5% specificity. We subsequently incorporate prior knowledge by ‘knowing’ the gene structure of one sequence and annotating the other conditional on it. Boosting accuracy close to perfect we demonstrate that conservation of gene structure on top of nucleotide sequence is a valuable source of information, especially in distantly related genomes.Availability: The Java code is available from the authors.Contact: degroot@stats.ox.ac.uk
Investigation on the association between atopic dermatitis and the development of mycosis fungoides in dogs: a retrospective case‐control study
Authors: Santoro D. , Marsella R. , Hernandez J. 
Published: March 2007

AbstractIn human medicine, the relationship between the immunodysregulation observed in atopic dermatitis (AD) and the development of mycosis fungoides (MF) has triggered considerable interest due to the increasing number of patients with MF who have a previous history of AD. The purpose of this retrospective case‐control study was to investigate whether dogs diagnosed with MF were more likely to have AD. The records of 96 000 canine patients at the University of Florida were searched. Inclusion criteria were a clinical and histological diagnosis of MF. Dogs admitted to the University of Florida, Veterinary Medical Center during the same time period (1991–2004) without a diagnosis of MF were included as controls. Four controls for each study dog were randomly selected (matched by year of admission). Frequency of AD and other exposure variables were compared among case and control dogs by using conditional logistic regression. Records of 19 dogs with a diagnosis of MF were identified. Five of them (5/19, 26.3%) had previous diagnosis of AD. The odds of having MF was 12 times (OR = 12.54; 95% CI = 1.95–80.39; P < 0.01) higher in dogs with AD than in dogs without AD. In conclusion, this study suggests an association between AD and MF in dogs. Future studies are necessary to confirm this finding and to investigate the pathogenic mechanisms involved in this association.
The impact of poor bowel preparation on colonoscopy: a prospective single centre study of 10 571 colonoscopies
Authors: Hendry P. O. , Jenkins J. T. , Diament R. H. 
Published: March 2007

AbstractObjective  Colonoscopy is regarded as the most sensitive method of evaluating the colon. Inadequate preparation reduces sensitivity and has adverse implications for individual patients and the Heath Service.Method  Data concerning the adequacy of bowel preparation and colonoscopy completion rates were prospectively collected on all colonoscopies performed in a single centre between January 1996 and January 2005. In addition, the strategy of further investigation in the event of incomplete examination was assessed.Results  A total of 10 571 colonoscopies were assessed and poor bowel preparation was identified in 1788 of these cases (16.9%). The completion rate was 67.5% in those with satisfactory preparation. In patients with poor preparation, 36% of colonoscopies were complete. Incomplete examination was more likely with poor preparation [OR = 3.76 (95% CI, 3.38–4.18), P = 0.0005]. Poor preparation was more likely for inpatients [OR = 3.54 (95% CI 3.14–3.96), P = 0.0005]. Even with satisfactory preparation, inpatient completion rates were significantly less [OR = 1.78 (95% CI, 3.14–3.96), P = 0.0005). A further 542 diagnostic procedures were undertaken in the poor preparation group, an additional £101 950 (€149 459) in expenditure.Conclusion  This study supports the view that inpatients fare badly. This is partly explained by higher rates of poor preparation; however, completion rates were reduced even with adequate preparation. Failed investigation and prolonged hospital stay increase cost. Colonoscopy completion rates need to be improved with particular attention to inpatients.
The impact of surgeon and pathologist on lymph node retrieval in colorectal cancer and its impact on survival for patients with Dukes’ stage B disease
Authors: Evans M. D. , Barton K. , Rees A. , Stamatakis J. D. , Karandikar S. S. 
Published: March 2007

AbstractObjective  An adequate lymph node harvest is necessary for accurate Dukes’ stage discrimination in colorectal cancer. The aim of this study is to identify the effect of variables, including the individual surgeon and pathologist, on lymph node harvest in a single institution.Method  Three hundred and eighty one consecutive patients had resection for colorectal cancer, in a single unit. Factors influencing lymph node retrieval, including individual surgeon and reporting pathologist, were subjected to uni‐ and multivariate analysis. Actuarial survival of all patients with Dukes’ stage B and C disease was then calculated and survival compared between Dukes’ stage B and C at differing levels of lymph node harvest.Results  The unit median lymph node harvest was 13 nodes/patient (95% CI 13.1–14.5). There was no difference in lymph node harvest between specialist colorectal surgeons and the pooled results of four nonspecialist consultant surgeons. However, there was a significant difference between reporting pathologists (P < 0.001). On univariate analysis, operation type, operative urgency, Dukes’ stage, T‐stage, reporting pathologist and use of neoadjuvant therapy in rectal cancer, were found to significantly affect lymph node retrieval. On multivariate analysis, operation type, T‐stage, reporting pathologist and neoadjuvant therapy in rectal cancer remained significant variables. Patients with one or more lymph node metastasis had greater nodal harvests than those without (median 15 vs 12 P = 0.02). Survival of patients with Dukes’ stage B disease was found to improve as lymph node harvest increased.Conclusion  Overall lymph node harvest, in this unit, varied according to the reporting pathologist but not operating surgeon. As lymph node harvest increased to 15 per patient, the probability of identifying a metastatic node increased.
Cytochrome P450 2B6 (CYP2B6) G516T influences nevirapine plasma concentrations in HIV‐infected patients in Uganda
Authors: Penzak SR , Kabuye G , Mugyenyi P , Mbamanya F , Natarajan V , Alfaro RM , Kityo C , Formentini E , Masur H 
Published: March 2007

ObjectivesPolymorphisms in the cytochrome P450 (CYP) 2B6 gene have been shown to influence nevirapine plasma concentrations in HIV‐infected European Caucasians. Although nevirapine is used extensively in Africa, the influence of CYP2B6 genotype on nevirapine exposure has not been assessed in this population. We aimed to determine the influence of CYP2B6 genotype at position 516 on nevirapine trough concentrations in HIV‐infected patients in Kampala, Uganda. Additional polymorphisms in the CYP and multidrug resistance protein‐1 (MDR‐1) genes were also assessed for their impact on nevirapine concentrations.MethodsThe following genotypes were determined in all subjects using polymerase chain reaction–restriction fragment length polymorphism: CYP2B6 G516T, MDR‐1 C3435T and G2677T, CYP3A4*1B and CYP3A5*3. Nevirapine plasma concentrations were determined using high‐performance liquid chromatography in 23 HIV‐infected patients who were generally healthy and had been taking nevirapine 200 mg twice daily for at least 14 days. Analysis of variance with post hoc testing was used to compare nevirapine concentrations among CYP2B6 genotype groups.ResultsThe median nevirapine trough concentration in individuals homozygous for the variant allele (TT) was 7607 ng/mL vs 4181 and 5559 ng/mL for GG and GT individuals, respectively (GG vs TT median ratio=1.82;P=0.011). The mean ratio for TT vs GG individuals (95% confidence interval) was 1.51 (1.18, 1.84). No associations were observed between the other polymorphisms studied and nevirapine concentrations.ConclusionsCYP2B6 G516T significantly influenced nevirapine trough concentrations in HIV‐infected patients in Uganda. Additional studies in larger patient populations are necessary to further define the potential clinical impact of these preliminary findings.
HIV‐associated Isospora belli infection: incidence and risk factors in the French Hospital Database on HIV
Authors: Guiguet M , Furco A , Tattevin P , Costagliola D , Molina J‐M ,   the French Hospital Database on HIV Clinical Epidemiology Group
Published: March 2007

ObjectiveTo determine the incidence of Isospora belli infection in HIV‐infected patients in France, and to study risk factors.MethodsThe French Hospital Database on HIV (FHDH) is a prospective cohort study that collects demographic, clinical and therapeutic data on patients managed in 62 hospitals. We reviewed all cases of I. belli infection recorded between 1992 and 2003. We compared the incidence in 1992–1994 [before the use of dual therapy and combination antiretroviral therapy (cART)] and in 1997–2003 (when use of cART was widespread), after stratification for CD4 cell count (< 50, 50–99, 100–199 and > 200 cells/μL).ResultsA total of 164 patients had I. belli infection either at enrolment (n=71) or during follow up (n=93). During the study period, I. belli infection tended to occur less frequently during follow up, and to be diagnosed mainly at database enrolment. The incidence of I. belli infection during follow up fell by 79% [relative hazard (RH) 0.21; 95% confidence interval (CI) 0.13–0.33] in the cART period compared with the pre‐cART period; no such change was noted among patients with CD4 cell counts below 50 cells/μL. In multivariable analysis, the risk of I. belli infection was significantly higher among patients from sub‐Saharan Africa (RH 4.3; 95% CI 2.6–7.3). After adjustment for CD4 cell count, patients receiving cotrimoxazole prophylaxis were found to be at a lower risk of I. belli infection (RH 0.3; 95% CI 0.2–0.6).ConclusionsIn France, I. belli infection among HIV‐infected patients is now mainly seen in patients from sub‐Saharan Africa, who present at an advanced stage.
Carotid intima–media thickness in HIV patients treated with antiretroviral therapy
Authors: Lebech Anne‐Mette , Wiinberg Niels , Kristoffersen Ulrik Sloth , Hesse Birger , Petersen Claus Leth , Gerstoft Jan , Kjær Andreas 
Published: March 2007

SummaryIntroduction:  Increased cardiovascular risk in HIV patients in antiretroviral therapy (ART) may be due to HIV infection, direct effect of ART or dyslipidaemia induced by ART. Our aim was to study the relative importance of HIV, ART and dyslipidaemia on atherosclerosis, assessed by the comparison of carotid artery intima–media thickness (IMT) in non‐smoking HIV patients with high or low serum cholesterol levels as well as in healthy volunteers.Methods : HIV patients in ART with normal cholesterol (≤5·5 mmol l−1; n = 13) or high cholesterol (≥6·5 mmol l−1; n = 12) as well as healthy controls (n = 14) were included. All were non‐smokers and had never received medication for dyslipidaemia or hypertension. IMT was measured by ultrasonography.Results : In HIV patients with normal cholesterol (≤5·5 mmol l−1), in HIV patients with hypercholesterolaemia (≥6·5 mmol l−1) and in controls (5·1 ± 0·9 mmol l−1) IMT were 683 ± 119, 656 ± 99 and 657 ± 99 μm, respectively. Thus no difference in IMT was found between the three groups. IMT values did not differ between patients receiving and not receiving protease inhibitors (658 ± 117 μm versus 687 ± 97 μm, P>0·05). In HIV patients IMT correlated inversely with HDL cholesterol levels (r = −0·50; P = 0·01), whereas no correlation was found with total cholesterol or LDL cholesterol.Conclusions : In non‐smoking HIV patients receiving ART no sign of accelerated atherosclerosis was found as assessed by IMT even not in hypercholesterolaemic HIV patients. IMT correlated with HDL cholesterol but not with LDL cholesterol. Based on these observations, one could speculate whether selective lowering of LDL cholesterol will be successful in reducing cardiovascular risk in non‐smoking HIV patients.
Effects of amino nitrogen on fermentation parameters by mixed ruminal microbes when energy or nitrogen is limited
Authors: KAJIKAWA Hiroshi , TAJIMA Kiyoshi , MITSUMORI Makoto , TAKENAKA Akio 
Published: March 2007

ABSTRACTRuminal microbes harvested from a ruminally fistulated cow were incubated in simple batch and semicontinuous cultures with NH3‐N or amino‐N on nitrogen‐ or energy‐excess diets in quantity (HN and LN diets, respectively, consisting of timothy hay plus soybean meal, or corn grain), based on evaluation with the National Research Council and Cornell Net Carbohydrate and Protein System models. In a batch culture experiment, supplementation with amino‐N promoted digestion and fermentation in the course of incubation (4–24 h) on both diets, but these effects mostly disappeared when the diets were sufficiently digested (at 48 h). In a semicontinuous culture experiment using Rusitec, no effect of amino‐N was exhibited after sufficient fermentation and digestion, but significant promotion of digestion was shown in the course of incubation on the HN diet, while no such effect was detected on the LN diet. The microbial yield for 24 h did not show a significant difference between the N sources of either of the two diets. These results suggest that the stimulatory effects of amino‐N are diminished when the diets are sufficiently digested after a long retention and incubation, and also that the effectiveness of amino‐N does not require a quantitatively energy‐excess status.
Advanced molecular immunoassay system for immunobiotic lactic acid bacteria using a transfectant of Toll‐like receptor 2
Authors: TOHNO Masanori , SHIMOSATO Takeshi , KAWAI Yasushi , ASO Hisashi , IKEGAMI Shuji , TAKETOMO Naoki , SAITO Tadao , KITAZAWA Haruki 
Published: March 2007

ABSTRACTToll‐like receptor 2 (TLR2) is a receptor for a variety of microbial components, and it also mediates activation signals in the cell relating to the innate immune system. In order to evaluate the precise molecular immunoregulation by various strains of lactic acid bacteria (LAB) via TLR2, the swine TLR2 (sTLR2)‐expressing transfectant was constructed using human embryonic kidney (HEK) 293 cells. It is demonstrated that intact immunobiotic LAB can induce immune responses through TLR2, and that different nuclear factor‐κB (NF‐κB) activities of various strains can be accurately detected by sTLR2‐expressing HEK293 cells. Furthermore, cellular activation of NF‐κB via TLR2 is reflected in enhanced binding and uptake of LAB. The sTLR2‐expressing HEK293 cells were also useful for characterizing the expression pattern of type I helper T (Th1) and type II helper T (Th2) cytokines by the stimulation of immunobiotic LAB. These results suggest that sTLR2‐expressing HEK293 cells may be useful in certain molecular immunoassay systems for producing new physiologically functional foods with intestinal immunomodulatory abilities, such as the maintenance of Th1/Th2 polarization.
Overweight and obesity among affluent Bengalee schoolgirls of Lake Town, Kolkata, India
Authors: Bose Kaushik , Bisai Samiran , Mukhopadhyay Ashish , Bhadra Mithu 
Published: March 2007

AbstractA cross‐sectional study was undertaken to determine the prevalence of overweight and obesity among 431 Bengalee schoolgirls aged 6–9 years in Kolkata, India. Anthropometric measurements of height and weight were made on 431 girls. The body mass index (BMI) was computed following the standard equation. Overweight and obesity was defined following the internationally accepted BMI cut‐off points. Results revealed that the overall rates of overweight and obesity were 17.63% and 5.10%, respectively. A steady increase in number of overweight individuals was observed from 6 to 9 years. The prevalence of overweight among affluent Bengalee children was higher than those reported from other Asian countries.
A survey of neonatal nutrition policies and practices in the UK and Eire
Authors: Tuthill David P. ,   Child Nutrition Panel
Published: March 2007

AbstractOptimal nutrition is one of the fundamental components for infants to reach their full growth and neurodevelopmental potential. Best practice is facilitated by a contemporaneous, multidisciplinary, evidence‐based nutrition policy. Such evidence has recently been reviewed. We have assessed: the prevalence of nutrition policies in neonatal units in the UK and Eire; their application to hypothetical cases; the availability of dietetic input; and whether any differences existed between non‐regional and regional units. A standardized questionnaire was devised by a multidisciplinary group and posted to all 255 neonatal units in the UK and Eire in 2002. Replies from 67 neonatal units were received: 48 out of 233 non‐regional and 19 out of 22 regional units. A feeding policy was present in 33 units, and regular access to dietitians occurred in 37 units. For a hypothetical infant less than 28 weeks’ gestation, enteral feeds would be commenced at 0–2 days in 81% of non‐regional and 94% of regional units (P = ns), and be continuous in 11% of non‐regional and 32% of regional units, and bolus feeding in 89% of non‐regional and 68% of regional units (P = ns). Routine fortification of breastmilk would occur more frequently in non‐regional units (96%) than in regional units (79%) (P = 0.050). Vitamin and iron supplements would be given to infants receiving postdischarge or high‐energy milks in 68% of non‐regional units and in 79% of regional units (P = ns). Calorie counts (63% regional vs. 8% non‐regional, P < 0.001), and daily weights (68% regional vs. 33% non‐regional, P = 0.014), were used more frequently in regional units. Many units surveyed did not have a nutrition policy. Many infants receive unnecessary additional vitamins and supplements. Practice is variable throughout the country, but we found no evidence of major differences between regional and non‐regional units, apart from their monitoring of growth and rates of breastmilk fortifier usage.
CARD15 variants determine a disturbed early response of monocytes to adherent‐invasive Escherichia coli strain LF82 in Crohn's disease
Authors: Peeters H. , Bogaert S. , Laukens D. , Rottiers P. , De Keyser Filip , Darfeuille‐Michaud A. , Glasser A.‐L. , Elewaut D. , De Vos M. 
Published: March 2007

SummaryCaspase activation and recruitment domain 15 (CARD15) and Toll‐like receptor 4 (TLR4) are respectively intracellular and membrane‐bound receptors for bacterial cell wall components [respectively muramyl dipeptide (MDP) and lipopolysaccharide (LPS)]. Polymorphisms in CARD15 and TLR4 have been linked with Crohn's disease (CD). Adherent‐invasive Escherichia coli (AIEC) strains with particular adhesion and invasion characteristics have been specifically associated with CD ileal mucosa. The aim of this study was to investigate the functional impact of these polymorphisms on monocytes in patients with CD, in response to MDP, LPS and AIEC strain LF82. Monocytes were isolated from 40 patients with CD using magnetic cell sorting, stimulated with LPS or MDP or infected with AIEC. IL‐1β, IL‐6, IL‐8, IL‐10, IL‐12 and tumour necrosis factor alpha induction was assessed using quantitative real time–polymerase chain reaction, Cytometric Bead Array and ELISA. Bacterial intracellular survival and replication was assessed using a gentamicin protection assay. Results were linked with the presence of CARD15 and TLR4 polymorphisms. Monocytes of patients with CARD15 polymorphisms showed an early reduced cytokine response (IL‐1β, IL‐6 and IL‐10) to infection with AIEC, which was restored after 20 h. A gene–dose effect was seen, comparing wild‐types, heterozygotes and homozygotes. We found no differences in intracellular survival and replication of AIEC. Heterozygous carriage of TLR4 polymorphisms did not influence monocyte response. In conclusion, patients with CD carrying CARD15 polymorphisms show a disturbed early inflammatory monocyte response after infection with AIEC strain LF82. For the first time, a functional defect was detected in single heterozygous carriers. These findings reflect the potential role of a genetically altered host response to disease‐related bacteria in the pathogenesis of CD.