bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteria and viruses in the water column of tropical freshwater reservoirs
Authors: Peduzzi Peter , Schiemer Fritz 
Published: June 2004

SummaryIn tropical freshwater reservoirs of Sri Lanka, which are linked in an aquatic network, bacterial abundance and production as well as virus abundance, frequency of viral infection and virus production were investigated together with a set of nutrient species (Kjeldahl‐N, NO3‐N, total P, soluble P, PO4‐P). At two characteristic seasons (wet season, dry season), samples were taken from two types of reservoirs (new upland impoundment and ancient, shallow lowland reservoir), each during 4 days at various depths of the entire water columns. Kjeldahl‐N and total P were greatly elevated in the wind‐mixed water body of the shallow impoundment during the dry season, whereas the deeper reservoir type exhibited no obvious seasonality. In SYBR green™‐stained samples, bacterial abundance showed no seasonal pattern in either reservoir type. Bacterial secondary production, however, was significantly elevated in the entire water column of the shallow impoundment under wind‐mixed conditions in the dry season. Highest abundance of virus particles and elevated frequency of bacteria containing mature phages were also observed in the shallow reservoir during the dry season indicating favourable conditions for virus propagation. Data from this aquatic network show that most virus parameters, such as abundance or frequency of visibly infected cells, were positively linked to bacterial abundance and production, but also to organic nitrogen or some phosphorus species. We calculated that between 13.2% and 46.1% of the bacterial standing stocks would be subjected to virus‐mediated mortality. Estimates of bacteriophage production revealed that from 10 × 109 up to 98 × 109 phages were produced per litre and day. Bacteria and viruses in the studied tropical freshwater system appear to be linked to various environmental conditions and may affect processes at the ecosystem scale.
Free Shiga toxin bacteriophages isolated from sewage showed diversity although the stx genes appeared conserved
Authors: Muniesa M. , Serra‐Moreno R. , Jofre J. 
Published: June 2004

SummaryPhages carrying the stx2 gene were detected in a range of sewage samples using a plaque hybridization‐based method. After detection, phages were isolated and propagated with a laboratory strain of Escherichia coli as host for characterization purposes. Although it was not possible to conduct propagation or transduction experiments on most of the phages, 11 reached a sufficiently high titre for studies of host infectivity, electron microscopy and sequencing of the stx2 flanking regions to be performed. These phages showed a wide range of host infectivity and morphology. The genetic structure of the 5′stx flanking region appeared conserved whereas the 3′ region differed from that of previously described phages. This is the first description of infectious stx‐phages isolated as free particles in the environment, and as such constitutes a new contribution to the study of the ecology of these phages.
Adaptation of sympatric Achromatium spp. to different redox conditions as a mechanism for coexistence of functionally similar sulphur bacteria
Authors: Gray Neil D. , Comaskey Daria , Miskin Ian P. , Pickup Roger W. , Suzuki Keiko , Head Ian M. 
Published: June 2004

SummaryChanges in the abundance of sympatric Achromatium spp. in response to the artificial manipulation of redox conditions in sediment microcosms was determined by fluorescence in situ hybridization (FISH). Adaptation to different redox conditions was shown to be one mechanism that supported the coexistence of functionally similar Achromatium spp. In sediment microcosms, in which the overlying water was oxygenated, Achromatium community size and composition remained unchanged over time. However, imposition of anoxic conditions induced changes in community structure. Anoxia caused a reduction in the relative abundance of Achromatium sp. RY8 (72 ± 4% to 49 ± 2%) and an increase in Achromatium sp. RY5 (19 ± 5% to 32 ± 3%) and a newly identified Achromatium sp., RYKS (14 ± 4% to 27 ± 2%). In anoxic microcosms supplemented with a single addition of nitrate at different initial concentrations the relative decline in Achromatium sp. RY8 was dependent on the initial nitrate concentration. In these experiments nitrate was rapidly removed. In contrast, when high levels of nitrate were maintained by periodic replacement of the overlying water with nitrate supplemented anoxic water, the composition of the Achromatium community remained stable over time. This suggested that all of the coexisting Achromatium spp. are obligate or facultative anaerobes, but, Achromatium sp. RY8 was more sensitive to sediment redox conditions than the other Achromatium species. Given the heterogeneous nature of sedimentary environments, redox‐related niche differentiation may promote coexistence of sympatric Achromatium spp.
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
Authors: Santos Scott R. , Ochman Howard 
Published: June 2004

SummaryMolecular characterizations of bacteria often employ ribosomal DNA (rDNA) to establish the identity and relationships among organisms, but the use of rRNA sequences can be problematic as the result of alignment ambiguities caused by indels, the lack of informative characters, and varying functional constraints over the molecule. Although protein‐coding regions have been used as an alternative to rRNA, there is neither consensus among the genes examined nor ways to rapidly obtain sequence information for such genes from uncharacterized bacterial species. To standardize the set of protein‐coding loci assayed in bacterial genomes, we examined over 100 widely distributed genes to identify sets of universal primers for use in the PCR amplification of protein coding regions that are common to virtually all bacteria. From this set, we developed primer sets that each target of 10 genes spanning an array of genomic locations and functional categories. Although many of the primers contain sequence degeneracies that aid in targeting genes across diverse taxa, most are adequate for direct sequencing of amplification products, thereby eliminating intermediate cloning before sequence determination. We foresee the analysis of these protein‐coding regions as being complementary to ribosomal DNA for answering questions pertaining to bacterial identification, classification, phylogenetics and evolution.
Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH)
Authors: Urzì Clara , La Cono Violetta , Stackebrandt Erko 
Published: June 2004

SummaryBacteria of the family of Geodermatophilaceae are actively involved in the decay processes [Urzì, C. and Realini, M. (1998) Int Biodeterior Biodegrad 42: 45–54; Urzì, C., Salamone, P., Schumann, P., and Stackebrandt, E. (2000) Int J Syst Evol Microbiol 50: 529–536] of stone monuments. Characterization of isolates includes phenotypic, chemotaxonomic and genetic analysis often requiring long‐term procedures. The use of specific probes for members of Geodermatophilaceae family could be useful for the easy detection of those strains colonizing rock surfaces and involved in the biodeterioration. Two 16S rRNA‐targeted oligonucleotide probes were designed for the specific detection of members of the family Geodermatophilaceae using fluorescence in situ hybridization (FISH); one probe specific for members of the two genera Geodermatophilus/Blastococcus and the second for members of the genus Modestobacter.
Analysis of Factors Influencing Taiwan's Unregistered Overseas Investment Behavior
Authors: Yang Ya‐Hwei , Tu Ying‐Yi 
Published: June 2004

There has been a significant increase in Taiwanese investment overseas since the mid‐1980s. However, when Taiwanese investors choose to pursue overseas investment, they do not necessarily register this with the government (specifically, with the Investment Commission at the Ministry of Economic Affairs). Although this is a common phenomenon, there has thus far been a scarcity of in‐depth analysis of this trend within the published literature. The official statistics on Taiwanese overseas investment, as provided by the Taiwanese government, differ significantly from those provided by the countries in which the investments take place. We can deduce from this that some businessmen engage in foreign investment without registering it with the government, and as a consequence, suggest that the reasons for such non‐registering behavior are worthy of study.This paper adopts theoretical and empirical models to observe unregistered overseas investment behavior patterns and to investigate the reasons influencing the decision to engage in unregistered investment. A questionnaire survey is under‐taken to estimate the proportion of unregistered investment, with theoretical and empirical analyses being used to explore the factors behind the decision to adopt non‐registering behavior. The results show that the proportion of unregistered investment tends to be higher in South‐East Asia and China than in the USA and that complicated administrative procedures have a positive influence on this type of behavior. Furthermore, such behavior can be predetermined by the prospects of higher returns on investment.
NAD – new roles in signalling and gene regulation in plants
Authors: Hunt Lee , Lerner Felicitas , Ziegler Mathias 
Published: June 2004

SummaryThe pyridine nucleotides, NAD+, NADH, NADP+, and NADPH have long‐established and well‐characterised roles as redox factors in processes such as oxidative phosphorylation, the TCA cycle, and as electron acceptors in photosynthesis. Recent years have seen an increase in the number of signalling and gene regulatory processes where NAD+ or NADP+ are metabolised. Cyclic ADP‐ribose (cADPR) and nicotinic acid adenine dinucleotide phosphate (NAADP) are metabolites of NAD+ and NADP+, respectively, and now have widely accepted roles as potent intracellular calcium releasing agents in animals, but are less well characterised in plants. NAD kinases catalyse the transfer of a phosphate group from ATP to NAD to form NADP and are well characterised in plants in their requirement for the calcium binding protein calmodulin, thereby putatively linking their regulation to stress‐induced intracellular calcium release. A second group of proteins unrelated to those above, the sirtuins (Sir2) and poly ADP‐ribose polymerases (PARPs), cleave NAD and transfer the ADP‐ribose group to acetyl groups and proteins, respectively. These have roles in transcriptional control and DNA repair in eukaryotes.

Contents

Summary

I.
Introduction
32

II.
NAD synthesis and breakdown
32

III.
cADPR in plants
34

IV.
NAADP in plants
35

V.
NAD kinases
35

VI.
NAD and gene regulation
37

VII.
Sir2 is an NAD dependant histone deacetylase
37

VIII.
Nicotinamidases
38

IX.
Poly ADP‐ribosylation
39

X.
Poly(ADP‐ribose) glycohydrolase (PARG)
40

XI.
Subcellular compartmentation of NAD and NADP in plants
41

XII.
Conclusions
41

Acknowledgements
41

References
41
Gene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray system
Authors: Nagano Y , Nagahori K , Yoshiro F , Hamaguchi Y , Ishikawa T , Ichikawa Y , Togo S , Okazaki Y , Hayashizaki Y , Shimada H 
Published: June 2004

Abstract: Aims: We assessed changes in gene expression of hypertrophied liver after portal vein ligation (PL) in a test group of rats compared to a control group, which had the same size liver but no PL.Methods: The portal veins of the left and median lobes in the test group were ligated in an initial operation. Four days after the PL, the liver volume of the posterior caudate lobe (5%) increased two‐fold and comprised 10% of the liver. A 90% hepatectomy was then performed, leaving only the hypertrophied posterior caudate lobe, and leaving the normal anterior and posterior caudate lobes (10%) in the control (sham) group. A comparison of the expression profiles between two groups was performed using cDNA microarrays and the hepatic ATP level was measured.Results: The survival rate for the PL group was significantly higher than for the sham group at 4 days after the hepatectomy (56.3% and 26.7%, P<0.05). Gene expression of cyclin D1, proliferating cell nuclear antigen, cyclin A and B was upregulated, and the cyclin‐dependent kinase inhibitor was downregulated. Increases were observed in: (i) pyruvate dehydrogenase, the tricarboxylic acid cycle cycle regulator, (ii) acyl‐CoA dehydrogenase, the oxidation regulator, and (iii) cytochrome oxidases, the oxidative phosphorylation regulator. Hepatic ATP concentration after hepatectomy was better maintained in the PL group than in the sham group (0.48±0.01 μmol/ml vs. 0.33±0.01 μmol/ml, P<0.05).Conclusion: The regenerating liver increased tolerance for extended hepatectomy compared to normal liver. It is believed that this is because the induced rapid regeneration of the remaining liver after hepatectomy increases ATP metabolism.
Biochemical markers of liver fibrosis and lymphocytic piecemeal necrosis in UDCA‐treated patients with primary biliary cirrhosis
Authors: Corpechot Christophe , Poujol‐Robert Armelle , Wendum Dominique , Galotte Marie , Chrétien Yves , Poupon Renée Eugénie , Poupon Raoul 
Published: June 2004

Abstract: Background/Aim: We have previously shown that the histological stage and severity of lymphocytic piecemeal necrosis (LPN) are independent predictive factors of cirrhosis development in ursodeoxycholic acid (UDCA)‐treated patients with primary biliary cirrhosis (PBC). Our aim during this study was to determine whether biochemical parameters classically used in PBC management and measured under UDCA could be considered as reliable surrogate markers for these histological prognostic indices in clinical practice.Method: The study included 153 patients with PBC who had undergone a control liver biopsy after 2 years of UDCA therapy. The relationships between histological and biological features were assessed by variance analysis and logistic regression. The diagnostic value of independent markers was assessed in terms of their sensitivity, specificity, positive predictive value (PPV) and negative value (NPV) and receiver‐operating characteristic curves.Results: Two variables were independently associated with extensive fibrosis (i.e. advanced histological stages): serum levels of bilirubin and hyaluronic acid (HA). A fibrosis index ([bilirubin (μmol/l)/14]+[HA (μg/l)/143]) higher than 1.5 exhibited good PPV and specificity (>74%) but rather poor NPV and sensitivity (<64%) regarding a diagnosis of extensive fibrosis. The only independent marker of LPN was aspartate aminotransferase (AST) activity. AST activity of more than twice the upper limit of normal showed acceptable PPV (>70%) but very low sensitivity (<25%) for a diagnosis of LPN.Conclusions: Serum bilirubin and HA levels measured under UDCA therapy are of acceptable diagnostic value for extensive fibrosis, but none of the biochemical tests commonly employed in the management of PBC can be considered as surrogate markers of LPN. Taken together with our previous results, these findings suggest that liver biopsy may be necessary to screen UDCA‐treated patients who might require additional therapies.
Montelukast for Migraine Prophylaxis: A Randomized, Double‐Blind, Placebo‐Controlled Study
Authors: Brandes Jan L. , Visser W. Hester , Farmer Mildred V. , Schuhl Amy L. , Malbecq William , Vrijens France , Lines Christopher R. , Reines Scott A. ,   Protocol 125 study group
Published: June 2004

Objective.—To evaluate the efficacy and tolerability of montelukast 20 mg in the prophylactic treatment of migraine.Background.—A previous small open‐label study in migraine patients suggested prophylactic efficacy for montelukast, an antagonist of the cysteinyl leukotriene receptor that is used in the treatment of asthma. We sought to confirm these findings in a randomized controlled trial.Methods.—This multicenter, randomized, double‐blind, placebo‐controlled, parallel‐groups study enrolled adult migraine outpatients who experienced ≥3 and ≤8 migraine attacks per month for the last 6 months. Patients were entered into a 2‐month, single‐blind, placebo run‐in phase. Only patients who experienced ≥3 migraine attacks in the second month were eligible to enter the subsequent 3‐month, double‐blind treatment phase of the study. The primary efficacy endpoint was the percentage of patients reporting at least a 50% decrease in migraine attack frequency per month during the double‐blind treatment period (months 3‐5) compared to baseline (run‐in month 2).Results.—A total of 93 patients were randomized to montelukast 20 mg and 84 patients to placebo at the end of the placebo run‐in month 2; 76 patients on montelukast and 72 patients on placebo completed the double‐blind treatment period. Over 3 months of treatment, there was no significant difference between the two groups in the percentage of patients who reported at least a 50% decrease in migraine attack frequency per month: 15.4% for montelukast versus 10.3% for placebo (P= .304). In addition, montelukast 20 mg was not significantly superior to placebo on any of the secondary endpoints. There were no differences between treatment groups for adverse events.Conclusion.—Montelukast 20 mg was well tolerated in migraine patients but was not an effective prophylactic for prevention of migraine.
Evidence‐Based Diagnosis of Nontraumatic Headache in the Emergency Department: A Consensus Statement on Four Clinical Scenarios
Authors: Cortelli Pietro , Cevoli Sabina , Nonino Francesco , Baronciani Dante , Magrini Nicola , Re Giuseppe , De Berti Gianni , Manzoni Gian Camillo , Querzani Pietro , Vandelli Alberto ,   Multidisciplinary Group for Nontraumatic Headache in the Emergency Department
Published: June 2004

Objective.—To provide to emergency department (ED) physicians with guidelines for diagnosis of patients with nontraumatic headaches.Background.—Many patients present to an ED with the chief complaint of headache. Causes of nontraumatic headache include life‐threatening illnesses, and distinguishing patients with such ominous headaches from those with a primary headache disorder can be challenging for the ED physician.Conclusion.—We present a consensus statement aimed to be a useful tool for ED doctors in making evidence‐based diagnostic decisions in the management of adult patients with nontraumatic headache.Methods.—A multidisciplinary work performed an extensive review of the medical literature and applied the information obtained to commonly encountered scenarios in the ED.
The Effect of Weather on Headache
Authors: Prince Patricia B. , Rapoport Alan M. , Sheftell Fred D. , Tepper Stewart J. , Bigal Marcelo E. 
Published: June 2004

Objectives.—To assess headache patients' beliefs about how strongly weather affects their headaches; To objectively investigate the influence of multiple weather variables on headache.Design and Methods.—Our sample consisted of 77 migraineurs seen in a headache clinic, who provided headache calendars for a period ranging from 2 to 24 months. Our study was divided into two phases. First, each patient was given a questionnaire assessing their beliefs about how strongly (if so) weather affected their headaches. Second, weather data were collected from the National Weather Service, from three reporting stations central to the residences of the study participants. Analysis was performed on 43 variables to generate three meteorological factors. Linear regression was used to assess the relationship between headache and these three factors. Factor 1 represents a function of absolute temperature and humidity. Factor 2 represents a changing weather pattern. Factor 3 represents barometric pressure.Results.—Of the 77 subjects in the study, 39 (50.6%), were found to be sensitive to weather, but 48 (62.3%) thought they were sensitive to weather conditions (P < 0.05). Thirty (38.9%) were sensitive to one weather factor and 9 (11.7%) to two factors. Twenty‐six (33.7%) were sensitive to factor 1; 11 (14.3%) to factor 2; 10 (12.9%) to factor 3.Conclusions.—Our study supports the influence of weather variables on headache. We showed that patients are susceptible to multiple weather variables and that more patients thought weather was a trigger than was the case.
Spontaneous Intracranial Hypotension Syndrome: Report of Twelve Cases
Authors: Ferrante Enrico , Savino Anna , Sances Grazia , Nappi Giuseppe 
Published: June 2004

Purpose.—To investigate clinical, MRI, and radioisotope findings and therapeutic outcome of the syndrome of spontaneous intracranial hypotension (SIH).Background.—Spontaneous intracranial hypotension is characterized by orthostatic headache, low CSF pressure, and MRI findings of diffuse pachymeningeal gadolinium enhancement without previous history of head trauma or lumbar puncture. Spontaneous CSF leakage from a spinal dural tear has been suggested as the underlying pathogenic mechanism of SIH. Most patients recover without sequelae, but subdural collections have been described in a few.Methods.—Twelve consecutive patients (10 females, 2 males, mean age 39 years) with headache related to the syndrome of spontaneous intracranial hypotension were investigated.Results.—Eleven patients presented orthostatic headache, one patient had continuous nonpostural headache. Additional clinical symptoms included nausea, vomiting, tinnitus, diplopia, and back pain. All the patients had low CSF opening pressure, seven had increased CSF albumin, and four had pleocytosis. Brain MRI showed diffuse pachymeningeal gadolinium enhancement. Other features included subdural fluid collections (hematoma/hygroma) in four patients, downward displacement of the brain in four patients, and enlargement of the pituitary gland in one patient. Radioisotope cisternography results indicated, in two patients, a CSF leakage site in the cervico‐thoracic region, and in one patient showed limited ascent of the tracer to the cerebral convexity and early appearance of radioisotope in the bladder. All the patients had complete resolution of headache with conservative treatment.Conclusions.—Patients with SIH have distinct MRI and sometimes radioisotope cisternographic abnormalities and generally respond favorably to conservative management.