bluuebunny/crossref_metadata_2025_split huggingface dataset:
Skin and Environmental Contamination With Vancomycin-Resistant Enterococci in Patients Receiving Oral Metronidazole or Oral Vancomycin Treatment forClostridium difficile–Associated Disease
Authors: Sethi Ajay K. , Al-Nassir Wafa N. , Nerandzic Michelle M. , Donskey Curtis J. 
Published: December 2008

Background.Oral metronidazole has been recommended for treatment of mild-to-moderateClostridium difficile–associated disease (CDAD), in part because of concern that use of vancomycin may be more likely to promote colonization and transmission of vancomycin-resistant enterococci (VRE). The objective of our study was to compare the frequency of skin and environmental VRE contamination associated with metronidazole treatment for CDAD with such frequency associated with vancomycin treatment for CDAD.Design.Prospective, observational study. This study was performed at the Cleveland Veterans Affairs Medical Center (Cleveland, OH). For patients with CDAD who had concurrent VRE colonization, stool, skin, and environmental samples were cultured for VRE before, during, and up to 3 weeks after therapy with metronidazole or vancomycin. The proportions of skin and environmental contamination were compared before and after resolution of diarrhea and during treatment with metronidazole or vancomycin.Results.Of the 34 patients, 17 were treated with vancomycin and 17 were treated with metronidazole. The proportion of environmental cultures that were positive for VRE was significantly higher during resolution of diarrhea than it was after resolution of diarrhea (38% vs 28%;P= .025), whereas the proportion of skin cultures positive was not different during and after resolution of diarrhea (78% vs 71%;P= .60). There were no differences between patients who received metronidazole and patients who received vancomycin in the proportions of skin culture results (73% vs 77%;P= .80) or environmental culture results (37% vs 32%;P= .359) that were positive for VRE. Eleven patients (32%) had chronic fecal incontinence, and 28 (82%) had incontinence at least once during their CDAD episode.Conclusions.In VRE-colonized patients with CDAD who experienced frequent fecal incontinence, skin and environmental VRE contamination was common during and after resolution of diarrhea. The frequency of VRE contamination was similar between patients treated with metronidazole and patients treated with vancomycin.
Statistical catch-at-age analysis vs. ADAPT-VPA: the case of Gulf of Maine cod
Authors: Butterworth Doug S. , Rademeyer Rebecca A. 
Published: December 2008

Abstract
Butterworth, D. S., and Rademeyer, R. A. 2008. Statistical catch-at-age analysis vs. ADAPT-VPA: the case of Gulf of Maine cod. – ICES Journal of Marine Science, 65: 1717–1732. In 2003, given an estimate of a spawning-stock biomass (Bsp) of 27% of the maximum sustainable yield (MSY) level based on an adaptive framework-virtual population analysis (ADAPT-VPA) assessment using data only after 1981, the Gulf of Maine cod (Gadus morhua) stock was deemed “overfished” under the US Magnuson–Stevens Act. However, an alternative statistical catch-at-age assessment (SCAA) at the time, using survey data from 1964, indicated Bsp above . This is investigated, together with other (sometimes conflicting) suggestions made during a number of recent assessment reviews of this stock. The primary reason for the different result is that the ADAPT-VPA assessment imposed asymptotically flat selectivity-at-age when there was strong statistical evidence for dome-shaped selectivity. Once adjusted for this, either assessment method robustly estimates Bsp relatively close to rather than below the “overfished” threshold of 0.5 . SCAA allows the longer series of survey data available to be incorporated, providing a better basis to estimate MSY-related targets and doubling the related precision in some cases. As such targets are important when implementing the Magnuson–Stevens Act, SCAA seems preferable to ADAPT-VPA for assessing this stock. Some broader inferences to be drawn from this comparative process include the need for: (i) careful treatment of the plus-group, especially if selectivity may be dome-shaped; (ii) flexible parameterizations of selectivity-at-age in SCAA to avoid false perceptions of the precision of results; and (iii) care in the use of the Beverton–Holt stock–recruitment function, as it gives inappropriately low estimates of if there is an overall negative trend in the estimates of recruitment plotted against Bsp.
The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation
Authors: Goodsir Freya , Armstrong Michael J. , Witthames Peter R. , Maxwell David L. , Fox Clive J. 
Published: December 2008

Abstract
Goodsir, F., Armstrong, M. J., Witthames, P. R., Maxwell, D. L., and Fox, C. J. 2008. The use of species-specific TaqMan probes for identifying early stage gadoid eggs following formaldehyde fixation. – ICES Journal of Marine Science, 65: 1573–1577. Surveys of fish eggs are increasingly being used to monitor the spawning areas and stock status of commercially important species such as Atlantic cod (Gadus morhua), but early stage cod eggs are visually indistinguishable from those of several other common co-occurring species, including haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus). In recent surveys in the Irish and North Seas, a molecular identification technique (TaqMan multiplex real-time polymerase chain-reaction) assay has been used to overcome this problem. The method needs high-quality DNA, so the current protocol requires that individual “cod-like” eggs are “presorted” from plankton hauls on board ship and immediately preserved in ethanol. This increases seagoing staff costs, can be a difficult process at sea, and means that plankton sampling cannot be undertaken from non-specialized vessels such as fishing boats. Successful application of TaqMan probes to DNA from eggs preserved in formalin would overcome these problems, but previous attempts have resulted in poor success. In this study, batches of hatchery-sourced cod, haddock, and whiting eggs were fixed in 4% buffered formalin for up to 3 weeks, then transferred to a formaldehyde-free solution for 1, 2, or 3 months. After these periods they were assessed visually for fixation quality and analysed using species-specific TaqMan probes. Eggs, which had been fixed for up to 3 weeks in formalin, were identified successfully, although the positive rate (84–96%) was slightly lower than samples preserved throughout in ethanol (92–99%). There was no increase in the percentage of eggs misidentified comparing formalin-fixed and ethanol-preserved material. These results suggest that TaqMan probes can be applied successfully to fish eggs fixed in 4% buffered formalin for up to 3 weeks.
Has the fishery contributed to a major shift in the distribution of South African sardine?
Authors: Coetzee Janet C. , van der Lingen Carl D. , Hutchings Laurence , Fairweather Tracey P. 
Published: December 2008

Abstract
Coetzee, J. C., van der Lingen, C. D., Hutchings, L., and Fairweather, T. P. 2008. Has the fishery contributed to a major shift in the distribution of South African sardine? – ICES Journal of Marine Science, 65: 1676–1688. A major shift in the distribution of South African sardine (Sardinops sagax) has resulted in a significant spatial mismatch in fishing effort vs. fish abundance in recent years. The sardine fishery started on the west coast during the 1940s, and processing capacity there increased rapidly. This trend together with increases in annual landings continued up to the early 1960s, but then the fishery collapsed as a consequence of overfishing. The population then recovered steadily during the 1980s and 1990s, coincident with, but perhaps not entirely attributable to, the inception of conservative management practices, to support catches similar to pre-collapse levels. Since 2001, however, most of the sardine population has been situated on South Africa’s south coast, far from processing facilities. Fishing effort has increased concomitantly on that coast, particularly during the past three years, reflecting the continued decline in the abundance of sardine on the west coast. Three hypotheses explaining the change in the distribution of sardine have been proposed: (i) intensely localized (i.e. west coast) fishing pressure depleted that part (or functionally distinct unit) of the population; (ii) the shift was environmentally induced; and (iii) successful spawning and recruit survival on the south coast contributed disproportionately more towards the bulk of recruitment, and progeny spawned there now dominate the population and exhibit natal homing. The first of these hypotheses is evaluated, and management implications of the shift discussed.
The role of fatty acid hydrolase gene variants in inflammatory bowel disease
Authors: STORR M. , EMMERDINGER D. , DIEGELMANN J. , YÜCE B. , PFENNIG S. , OCHSENKÜHN T. , GÖKE B. , LOHSE P. , BRAND S. 
Published: December 2008

SummaryBackground  Recent studies suggest a role for the endocannabinoid system, including fatty acid amide hydrolase (FAAH), in intestinal inflammation.Aim  To analyse FAAH expression and the FAAH 385 C/A (p.Pro129Thr; rs324420) single nucleotide polymorphism (SNP) in‐patients with Crohn’s disease (CD) and ulcerative colitis (UC).Patients and methods  Genomic DNA from 1008 individuals (CD: n = 435; UC: n = 167; controls: n = 406) was analysed for the FAAH 385 C/A SNP. We determined FAAH mRNA expression by quantitative PCR in CD and UC lesions as well as in intestinal epithelial cells (IECs).Results  There were no significant differences regarding the frequency of this SNP in the three study groups (CD, UC, controls). However, CD patients homozygous for the FAAH p.Pro129Thr polymorphism were more likely to develop a severe disease phenotype associated with fistulas (P = 0.03, OR 3.12, 95% CI 1.08–8.98) and extra‐intestinal manifestations (P = 0.005, OR 4.29, CI 1.49–12.35). In UC, homozygous carriers had an earlier disease onset than wild‐type carriers (P = 0.01). FAAH mRNA expression correlated with IL‐8 mRNA expression in CD lesions (r = 0.53). However, pro‐inflammatory stimuli did not significantly increase FAAH mRNA expression in IECs.Conclusion  The FAAH p.Pro129Thr polymorphism may modulate the CD phenotype.
Impact of the haplotypes of the human pregnane X receptor gene on the basal and St John's wort‐induced activity of cytochrome P450 3A4 enzyme
Authors: Wang Xue‐Ding , Li Jia‐Li , Su Qi‐Biao , Guan Su , Chen Jie , Du Jun , He Yu‐Wen , Zeng Jun , Zhang Jin‐Xin , Chen Xiao , Huang Min , Zhou Shu‐Feng 
Published: December 2008

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Human pregnane X receptor (PXR/NR1I2) is a key regulator of cytochrome P450 3A4.• To date, there are 198 reported SNPs for the human PXR/NR1I2 gene.• Some of these SNPs are found to affect the inducing ability of PXR to CYP3A4. WHAT THIS STUDY ADDS • This study, for the first time, has investigated the effect of PXR haplotype on basal and St John's wort‐induced CYP3A4 activity in humans.• H1/H1 of the PXR gene had weaker basal transcriptional activity but greater inducible transcriptional activity to CYP3A4 than H1/H2 and H2/H2.AIMSHuman pregnane X receptor (PXR/NR1I2) is the master regulator of CYP3A4, which metabolizes >50% of drugs on the market. This study investigated the relationship between the two most frequent haplotypes [H1 (TCAGGGGCCACC) and H2 (CCGAAAACTAAT)] of PXR and basal and St John's wort (SJW)‐induced CYP3A4 activity.METHODSTen healthy subjects carrying H1 and H2 haplotypes (three subjects with H1/H1, four with H1/H2 and three with H2/H2) entered this study. The 10 subjects did not carry CYP3A4*4, *5 and *6. All subjects were administrated a 300‐mg SJW tablet three times daily for 14 days, and CYP3A4 activity was measured using nifedipine (NIF) as a probe. The plasma concentrations of NIF and dehydronifedipine (DNIF) were determined by a validated liquid chromatography/mass spectrometry/mass spectrometry method.RESULTSAfter administration of SJW, the AUC0–∞ of NIF decreased significantly, and the AUC0–∞ of DNIF increased significantly (P < 0.05). For H1/H2, the AUC0–∞ of NIF decreased by 42.4%, and the AUC0–∞ of DNIF increased by 20.2%; for H2/H2, the AUC0–∞ of NIF decreased by 47.9%, and the AUC0–∞ of DNIF increased by 33.0%; for H1/H1, the AUC0–∞ of NIF decreased by 29.0%, yet the AUC0–∞ of DNIF increased by 106.7%. The increase of the AUC0–∞ of DNIF in H1/H1 was significantly different from the other two haplotype pairs (P < 0.05). Meanwhile, before administration of SJW, the ratio of AUC0–∞(DNIF)/AUC0–∞(NIF) was the lowest for H1/H1 (22.1%), compared with H1/H2 (58.7%) and H2/H2 (30.0%).CONCLUSIONSH1/H1 of the human PXR gene had weaker basal transcriptional activity but greater inducible transcriptional activity to CYP3A4 than H1/H2 and H2/H2.
Brood conspicuousness and clutch viability in male‐caring assassin bugs (Rhinocoris tristis)
Authors: GILBERT JAMES , MANICA ANDREA 
Published: December 2008

Abstract 1. Conspicuousness to mates can bring benefits to both males (increased mating success) and females (reduced search costs), but also brings costs (e.g. increased predation and parasitism). Assassin bugs, Rhinocoris tristis, lay egg clutches either on exposed stems or hidden under leaves. Males guard eggs against parasitoids. Guarding males are attractive to females who add subsequent clutches to the brood. This is an excellent opportunity to study the effects of conspicuousness on the fitness of males and females.2. Using viable eggs in a multi‐clutch brood as a correlate of fitness, the present study examined whether laying eggs on stems affected (1) female fitness, through exposure to parasitism and cannibalism, and (2) male fitness, through attracting further females.3. Stem broods were more parasitised. However, males on stems accumulated more mates and more eggs, a net benefit even accounting for parasitism. The eggs gained from being on a stem were cannibalised. By contrast, higher mortality on stems suggests that females should gain by ovipositing on leaves. To the extent that egg viability represents fitness, male and female interests may therefore differ. This suggests a potential for sexual conflict that may affect other species with male care.4. Despite higher costs, females actually initiated more broods, and subsequently added bigger clutches to broods, on stems than under leaves. This suggests either that viable eggs do not reflect fitness, or that females laid in unfavourable locations. The key is now to address lifetime fitness, since unmeasured factors may affect offspring viability post‐hatching, and to investigate who controls the location of oviposition in R. tristis.
Functional association of cell death suppressor, Arabidopsis Bax inhibitor‐1, with fatty acid 2‐hydroxylation through cytochrome b5
Authors: Nagano Minoru , Ihara‐Ohori Yuri , Imai Hiroyuki , Inada Noriko , Fujimoto Masaru , Tsutsumi Nobuhiro , Uchimiya Hirofumi , Kawai‐Yamada Maki 
Published: December 2008

SummaryBax inhibitor‐1 (BI‐1) is a widely conserved cytoprotective protein localized in the endoplasmic reticulum (ER) membrane. We identified Arabidopsis cytochrome b5 (AtCb5) as an interactor of Arabidopsis BI‐1 (AtBI‐1) by screening the Arabidopsis cDNA library with the split‐ubiquitin yeast two‐hybrid (suY2H) system. Cb5 is an electron transfer protein localized mainly in the ER membrane. In addition, a bimolecular fluorescence complementation (BiFC) assay and fluorescence resonance energy transfer (FRET) analysis confirmed that AtBI‐1 interacted with AtCb5 in plants. On the other hand, we found that the AtBI‐1‐mediated suppression of cell death in yeast requires Saccharomyces cerevisiae fatty acid hydroxylase 1 (ScFAH1), which had a Cb5‐like domain at the N terminus and interacted with AtBI‐1. ScFAH1 is a sphingolipid fatty acid 2‐hydroxylase localized in the ER membrane. In contrast, AtFAH1 and AtFAH2, which are functional ScFAH1 homologues in Arabidopsis, had no Cb5‐like domain, and instead interacted with AtCb5 in plants. These results suggest that AtBI‐1 interacts with AtFAHs via AtCb5 in plant cells. Furthermore, the overexpression of AtBI‐1 increased the level of 2‐hydroxy fatty acids in Arabidopsis, indicating that AtBI‐1 is involved in fatty acid 2‐hydroxylation.
High‐resolution mapping revealed a 1.3‐Mbp genomic inversion in Ssi1, a dominant semidwarf gene in rice (Oryza sativa)
Authors: Miura K. , Wu J. , Sunohara H. , Wu X. , Matsumoto T. , Matsuoka M. , Ashikari M. , Kitano H. 
Published: December 2008

AbstractDwarf or semidwarf characters are an important trait for crop breeding as they provide lodging resistance. The rice mutant line DMF‐1 has a dm‐type semidwarf phenotype and high‐lodging resistance controlled by the dominant gene, Short second internode 1 (Ssi1). To elucidate the mechanism of reducing culm length in DMF‐1, we sought to identify the Ssi1 gene by positional cloning using the chromosome segment substitution line as a crossing parent. As a result of high‐resolution mapping, we found a 1.3‐Mbp genomic inversion and a newly arranged gene in the Ssi1 locus. In this study, we report the high‐resolution mapping and physical mapping of Ssi1. We also discuss the possible function of a novel rearranged Ssi1 gene for the dominant dm‐type semidwarf phenotype.
Gatifloxacin‐based triple therapy as a third‐line regimen for Helicobacter pylori eradication
Authors: Nishizawa Toshihiro , Suzuki Hidekazu , Nakagawa Izumi , Iwasaki Eisuke , Masaoka Tatsuhiro , Hibi Toshifumi 
Published: December 2008

AbstractBackground and Aim:  This study was designed to investigate the efficacy of gatifloxacin (GAT)–based triple therapy as a third‐line treatment for Helicobacter pylori (H. pylori) eradication, according to the assessment of the susceptibility to GAT and gyrA mutation.Methods:  Fourteen patients who had eradication failure following both clarithromycin‐based triple therapy and metronidazole‐based triple therapy, or who were infected with H. pylori isolates that were resistant to both clarithromycin and metronidazole after failure of clarithromycin‐based triple therapy, were enrolled. These patients were randomly assigned to two groups: (i) rabeprazole and amoxicillin (RA) and (ii) rabeprazole, amoxicillin, and GAT for 7 days (RAG). The minimal inhibitory concentrations were determined by the agar dilution method. The gyrA gene was examined by sequencing.Results:  The eradication rate was 0% in the RA group and 75% in the RAG group. The eradication rate in the RAG group was 100% in patients infected with GAT‐susceptible bacteria and/or bacteria without gyrA mutations, but was only 33.3% in those infected with GAT‐resistant bacteria or bacteria with gyrA mutations.Conclusion:  Although GAT may be a promising candidate for third‐line therapy, its selection must be based on the results of drug susceptibility testing or gyrA analyses.
Endoscopic survey of low‐dose‐aspirin‐induced gastroduodenal mucosal injuries in patients with ischemic heart disease
Authors: Nema Hiroaki , Kato Mototsugu , Katsurada Takehiko , Nozaki Youichi , Yotsukura Akihiko , Yoshida Izumi , Sato Katsuhiko , Kawai Yuko , Takagi Yasushi , Okusa Takanori , Takiguchi Shunichi , Sakurai Masayuki , Asaka Masahiro 
Published: December 2008

AbstractBackground and Aim:  Low‐dose aspirin is effective for the prevention of cardiovascular and cerebrovascular events, but the frequency of gastrointestinal injuries among users of low‐dose aspirin in Japan is currently unknown. In the present study endoscopic examination was performed to investigate the frequency of gastroduodenal injuries associated with low‐dose aspirin in patients with ischemic heart disease (IHD).Methods:  Screening upper endoscopic examinations were prospectively performed on 131 patients with IHD who were not receiving antiulcer treatment. Endoscopic findings such as ulcers and flat erosions were assessed as mucosal injuries.Results:  Mucosal injuries were found in 62 of 101 (61.4%) low‐dose aspirin users and three of 30 (10%) nonaspirin users. There were significantly more mucosal injuries among low‐dose aspirin users than among the non‐users (P < 0.0001). Gastroduodenal ulcers were found in 19 of 101 (18.8%) low‐dose aspirin users compared with one of 30 (3.3%) nonaspirin users. The frequency of mucosal injuries was not associated with the duration of aspirin treatment.Conclusion:  Endoscopy frequently reveals low‐dose aspirin‐induced gastroduodenal injuries in patients with IHD.
Correlations among total colonoscopic findings, clinical symptoms, and laboratory markers in ulcerative colitis
Authors: Osada Taro , Ohkusa Toshifumi , Okayasu Isao , Yoshida Tsutomu , Hirai Shu , Beppu Kazuko , Shibuya Tomoyoshi , Sakamoto Naoto , Kobayashi Osamu , Nagahara Akihito , Terai Takeshi , Watanabe Sumio 
Published: December 2008

AbstractBackground and Aim:  Colonoscopy plays an integral role in the diagnosis, management and surveillance of ulcerative colitis (UC). In the present study we assessed the relationship between endoscopic and histological findings, clinical symptoms, and laboratory data.Methods:  We performed total colonoscopy examinations in 54 consecutive patients with UC. Seven segments (appendiceal region, cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum) were scored for endoscopic and histological activity. The patients were also evaluated using a symptom‐activity index and laboratory markers: C‐reactive protein (CRP), erythrocyte sedimentation rate (ESR), and white blood cell (WBC) and platelet (plt) counts.Results:  There was a significant positive correlation between endoscopic and histological scores (rs = 0.738), and between symptom activity score, endoscopic score (rs = 0.444), and histological score (rs = 0.557). Although the endoscopic and histological scores of distal colonic lesions (rectum–sigmoid, endoscopic: rs = 0.515, histological: rs = 0.624) correlated with clinical symptoms, there was no similar correlation for the proximal colon (appendiceal region–descending; endoscopic, rs = 0.268, histological, rs = 0.329). CRP, ESR, and WBC count also correlated with the sum of endoscopic and histological scores (CRP, rs = 0.447, rs = 0.369; ESR, rs = 0.483, rs = 0.589; WBC, rs = 0.338, rs = 0.330), whereas platelet count did not (rs = 0.171, rs = 0.210). In partciular, CRP and ESR were well correlated with the activity of proximal colonic lesions (CRP, rs = 0.474, rs = 0.480; ESR, rs = 0.423, rs = 0.529) rather than with that of distal lesions (CRP, rs = 0.236, rs = 0.212; ESR, rs = 0.368, rs = 0.497).Conclusions:  In this study, clinical symptoms reflected the activity of distal colonic lesions, whereas CRP and ESR reflected the activity of proximal lesions. Therefore, total colonoscopy may be indicated when CRP or ESR is elevated in UC patients in clinical remission.