bluuebunny/crossref_metadata_2025_split huggingface dataset:
Part-of-speech tagging of Modern Hebrew text
Authors: BAR-HAIM ROY , SIMA'AN KHALIL , WINTER YOAD 
Published: May 2007

AbstractWords in Semitic texts often consist of a concatenation ofword segments, each corresponding to a part-of-speech (POS) category. Semitic words may be ambiguous with regard to their segmentation as well as to the POS tags assigned to each segment. When designing POS taggers for Semitic languages, a major architectural decision concerns the choice of the atomic input tokens (terminal symbols). If the tokenization is at the word level, the output tags must be complex, and represent both the segmentation of the word and the POS tag assigned to each word segment. If the tokenization is at the segment level, the input itself must encode the different alternative segmentations of the words, while the output consists of standard POS tags. Comparing these two alternatives is not trivial, as the choice between them may have global effects on the grammatical model. Moreover, intermediate levels of tokenization between these two extremes are conceivable, and, as we aim to show, beneficial. To the best of our knowledge, the problem of tokenization for POS tagging of Semitic languages has not been addressed before in full generality. In this paper, we study this problem for the purpose of POS tagging of Modern Hebrew texts. After extensive error analysis of the two simple tokenization models, we propose a novel, linguistically motivated, intermediate tokenization model that gives better performance for Hebrew over the two initial architectures. Our study is based on the well-known hidden Markov models (HMMs). We start out from a manually devised morphological analyzer and a very small annotated corpus, and describe how to adapt an HMM-based POS tagger for both tokenization architectures. We present an effective technique for smoothing the lexical probabilities using an untagged corpus, and a novel transformation for casting the segment-level tagger in terms of a standard, word-level HMM implementation. The results obtained using our model are on par with the best published results on Modern Standard Arabic, despite the much smaller annotated corpus available for Modern Hebrew.
Calculating modules in contextual logic program refinement
Authors: COLVIN ROBERT , HAYES IAN J. , STROOPER PAUL 
Published: May 2007

AbstractThe refinement calculus for logic programs is a framework for deriving logic programs from specifications. It is based on a wide-spectrum language that can express both specifications and code, and a refinement relation that models the notion of correct implementation. In this paper we extend and generalise earlier work oncontextual refinement. Contextual refinement simplifies the refinement process by abstractly capturing the context of a subcomponent of a program, which typically includes information about the values of the free variables. This paper also extends and generalisesmodule refinement. Amoduleis a collection of procedures that operate on a common data type; module refinement between a specification moduleAand an implementation moduleCallows calls to the procedures ofAto be systematically replaced with calls to the corresponding procedures ofC. Based on the conditions for module refinement, we present a method forcalculatingan implementation module from a specification module. Both contextual and module refinement within the refinement calculus have been generalised from earlier work and the results are presented in a unified framework.
Citrinin induces apoptosis via a mitochondria-dependent pathway and inhibition of survival signals in embryonic stem cells, and causes developmental injury in blastocysts
Authors: Chan Wen-Hsiung 
Published: May 2007

The mycotoxin CTN (citrinin), a natural contaminant in foodstuffs and animal feeds, has cytotoxic and genotoxic effects on various mammalian cells. CTN is known to cause cell injury, including apoptosis, but the precise regulatory mechanisms of CTN action, particularly in stem cells and embryos, are currently unclear. In the present paper, I report that CTN has cytotoxic effects on mouse embryonic stem cells and blastocysts, and is associated with defects in their subsequent development, both in vitro and in vivo. Experiments in embryonic stem cells (ESC-B5) showed that CTN induces apoptosis via ROS (reactive oxygen species) generation, increased Bax/Bcl-2 ratio, loss of MMP (mitochondrial membrane potential), induction of cytochrome c release, and activation of caspase 3. In this model, CTN triggers cell death via inactivation of the HSP90 [a 90 kDa isoform of the HSP (heat-shock protein) family proteins]/multichaperone complex and subsequent degradation of Ras and Raf-1, further inhibiting anti-apoptotic processes, such as the Ras→ERK (extracellular-signal-regulated kinase) signal transduction pathway. In addition, CTN causes early developmental injury in mouse ESCs and blastocysts in vitro. Lastly, using an in vivo mouse model, I show that consumption of drinking water containing 10 μM CTN results in blastocyst apoptosis and early embryonic developmental injury. Collectively, these findings show for the first time that CTN induces ROS and mitochondria-dependent apoptotic processes, inhibits Ras→ERK survival signalling via inactivation of the HSP90/multichaperone complex, and causes developmental injury in vivo.
Oxidative stress, antioxidant status and DNA damage in patients with impaired glucose regulation and newly diagnosed Type 2 diabetes
Authors: Song Fangfang , Jia Wenbo , Yao Ying , Hu Yafei , Lei Lin , Lin Jie , Sun Xiufa , Liu Liegang 
Published: May 2007

Previous studies have postulated the association between oxidative stress and Type 2 diabetes. Considering the long pre-diabetic period with IGR (impaired glucose regulation) and its high risk of developing diabetes, to test this hypothesis, we have investigated oxidative stress pathways and DNA damage in patients with IGR and newly diagnosed Type 2 diabetes. The study population consisted of 92 subjects with NGT (normal glucose tolerance), 78 patients with IGR and 113 patients with newly diagnosed diabetes. Plasma MDA (malondialdehyde) and TAC (total antioxidative capacity) status, erythrocyte GSH content and SOD (superoxide dismutase) activity were determined. A comet assay was employed to evaluate DNA damage. Compared with subjects with NGT, patients with IGR had reduced erythrocyte SOD activity. Patients with diabetes had a higher plasma MDA concentration, but a lower plasma TAC level and erythrocyte SOD activity, than the NGT group. Correlation analysis revealed a strong positive association between IR (insulin resistance) and MDA concentration, but negative correlations with TAC status and SOD activity. With respect to β-cell function, a positive association with TAC status and an inverse correlation with GSH respectively, were observed. The comet assay revealed slight DNA damage in patients with IGR, which was increased in patients with diabetes. Significant correlations were observed between DNA damage and hyperglycaemia, IR and β-cell dysfunction. In conclusion, the results of the present study suggest that hyperglycaemia in an IGR state caused the predominance of oxidative stress over antioxidative defence systems, leading to oxidative DNA damage, which possibly contributed to pancreatic β-cell dysfunction, IR and more pronounced hyperglycaemia. This vicious circle finally induced the deterioration to diabetes.
New Staging System for Sinonasal Inverted Papilloma in the Endoscopic Era
Authors: Cannady Steven B. , Batra Pete S. , Sautter Nathan B. , Roh Hwan‐Jung , Citardi Martin J. 
Published: May 2007

AbstractObjectives: Advanced endoscopic techniques have emerged as the preferred treatment modality for sinonasal inverted papilloma (IP); however, a staging system that provides prognostic information has not yet been developed. This study aims to develop a clinically relevant staging system for IP managed with the endoscopic approach as the primary surgical modality.Design: A systematic review of the English‐language literature (1985–2006) and a single institution's experience.Methods: From the literature, 445 patients with IP treated by endoscopic resection were identified in 14 reports. Only patients with known IP sites and outcomes were included.Results: Patients were categorized into three groups on the basis of recurrence rates (RR): group A (IP confined to the nasal cavity, ethmoid sinus, and medial maxillary sinus), 3.0% RR (n = 234); group B (IP with lateral maxillary sinus, sphenoid sinus, or frontal sinus involvement), 19.8% RR (n = 177); and group C (IP with extrasinus extension), 35.3% RR (n = 34). Pearson's chi‐square test showed statistically significant differences for all pair‐wise comparisons between groups (P < .05). Mean follow‐up was 39.8 months.Conclusions: This new staging system for IP provides information about prognosis (as operationally defined by RR) for IP managed by advanced endoscopic techniques. In contrast, other staging systems for IP reflect surgeon's judgment rather than outcomes data. This new classification for IP provides important objective data for preoperative planning and patient counseling.
Fusarium verticillioides GBB1, a gene encoding heterotrimeric G protein β subunit, is associated with fumonisin B1 biosynthesis and hyphal development but not with fungal virulence
Authors: SAGARAM UMA SHANKAR , SHIM WON‐BO 
Published: May 2007

SUMMARY Fusarium verticillioides (Sacc.) Nirenberg (teleomorph Gibberella moniliformis Wineland) is a maize pathogen that causes ear rots and stalk rots. The fungus also produces a group of mycotoxins, fumonisins, on infected ears, which cause considerable health and economic concerns for humans and animals worldwide. To date, our understanding of the molecular mechanisms associated with fungal virulence and fumonisin biosynthesis in F. verticillioides is limited. In this study, GBB1, a gene encoding a putative β subunit of a heterotrimeric G protein, was disrupted and the effects on fumonisin biosynthesis and virulence were evaluated. A GBB1 deletion mutant (Δgbb1) showed no significant differences in radial growth and mycelial mass but produced significantly less fumonisin B1 (FB1) than its wild‐type progenitor. HPLC analysis showed that Δgbb1 produced less than 10 p.p.m. FB1 while the wild‐type produced over 140 p.p.m. when strains were grown on cracked corn kernels. Reduced expression of the key FB1 biosynthetic genes, FUM1 and FUM8, in Δgbb1 provides further evidence that GBB1 is involved in FB1 regulation. Stalk rot virulence, as measured by mean lesion length and by area, was not significantly different in Δgbb1 compared with the wild‐type, suggesting that GBB1 does not regulate virulence in F. verticillioides. Developmentally, hyphae of Δgbb1 do not deviate from the original axis of polarity established upon germ tube emergence in contrast to wild‐type hyphae that meander on and off axis as they grow. Complementation of Δgbb1 with GBB1 restored FB1 production and hyphal growth to wild‐type. The results of this study demonstrate that heterotrimeric G protein β subunit plays an important role in regulation of FB1 biosynthesis and hyphal growth, but not virulence in F. verticillioides.
Tobacco NIMIN2 proteins control PR gene induction through transient repression early in systemic acquired resistance
Authors: ZWICKER SYLVIA , MAST SIMONE , STOS VLATKA , PFITZNER ARTUR J. P. , PFITZNER URSULA M. 
Published: May 2007

SUMMARYNPR1 (for Nonexpressor of PR genes; also known as NIM1) is a positive regulator of systemic acquired resistance (SAR) in Arabidopsis, which controls the induction of Pathogenesis‐Related (PR) genes by salicylic acid (SA). NPR1 interacts with members of two protein families, TGA transcription factors and NIMIN (for NIM1‐interacting) proteins. In Arabidopsis, NIMIN1, NIMIN2 and NIMIN3 constitute a small gene family of structurally related, yet distinct members. To unravel the biological significance of NIMIN interaction with NPR1, we searched a tobacco yeast two‐hybrid cDNA library for NPR1‐ and NIMIN2‐binding proteins. One NPR1 cDNA clone and three clones encoding NIMIN proteins were isolated. Although clearly similar to At NPR1, Nt NPR1 does not interact with At NIMIN3. Furthermore, all Nt NIMIN proteins identified are structurally related to At NIMIN2, thus forming a small NIMIN2 subfamily in tobacco. cDNA clones encoding At NIMIN1 or At NIMIN3 homologues were not identified. The function of NIMIN2 proteins was studied by expression of Nt NIMIN2a chimeric genes in tobacco. While constitutive NIMIN2a over‐expression delayed PR‐1 protein induction, suppression of NIMIN2 transcripts enhanced the accumulation of PR‐1 proteins. In both cases, the effects of altered NIMIN2 transcript levels became evident foremost early in SAR. Notably, Nt NIMIN2 gene expression is elevated prior to the induction of the PR‐1a gene. Together, the data suggest that, in tobacco, NIMIN2 proteins control PR‐1 gene expression, and that NIMIN2‐mediated control is exerted through transient PR‐1 repression before SAR has fully developed. Furthermore, although sharing conserved domains and functions, tobacco and Arabidopsis NPR1 and NIMIN proteins are clearly distinct.
Inflammatory status and kynurenine metabolism in rheumatoid arthritis treated with melatonin
Authors: Forrest Caroline M. , Mackay Gillian M. , Stoy Nicholas , Stone Trevor W. , Darlington L. Gail 
Published: May 2007

What is already known about this subject • There is good evidence that oxidative stress, associated with the generation of free radicals, is a major contributor to joint damage in rheumatoid arthritis.• It is also well established that melatonin is one of the most powerful, endogenous free radical scavengers, and it is very safe for human use.• We have therefore examined whether melatonin might be a useful adjunctive compound with which to treat arthritis. What this study adds • Once‐nightly administration of melatonin increases concentrations of some inflammatory markers, but patients experience no significant improvement in symptoms and no changes of proinflammatory cytokine concentrations.• Melatonin is an effective antioxidant, but because it is either not sufficiently effective, or it has some proinflammatory activity, it is not likely to prove beneficial in patients.AimSince melatonin is antioxidant and has some anti‐inflammatory actions, we have tested it as adjunctive treatment in patients with rheumatoid arthritis, to determine whether it can improve patients' symptoms.MethodsA total of 75 patients were allocated randomly to receive melatonin 10 mg at night in addition to ongoing medication, or a placebo of identical appearance. Monthly blood samples were taken and disease severity assessed over 6 months, plasma being analysed for inflammatory indicators [C‐reactive protein, erythrocyte sedimentation rate (ESR), neopterin], proinflammatory cytokines [interleukin (IL)‐1β, IL‐6, tumour necrosis factor (TNF)‐α], lipid peroxidation products and the kynurenine pathway metabolites of tryptophan.ResultsAn increase of ESR (two‐way anova F(1,127) = 5.24, P = 0.024) and neopterin concentrations (F(1,136) = 4.64, P = 0.033) was observed in treated patients compared with controls, reflected also in a significant trend for both to decline in placebo‐treated patients (P = 0.022), but not the melatonin‐treated group. Peroxidation products showed a significant trend to decrease in placebo‐ but not melatonin‐treated patients. These results suggest a proinflammatory action, but there were no significant effects of melatonin treatment on clinical assessments of patient symptoms or the concentrations of three proinflammatory cytokines, IL‐1β, IL‐6 and TNF‐α. Melatonin significantly increased plasma kynurenine concentrations (F(1,124) = 4.24, P = 0.041), again suggesting proinflammatory activity.ConclusionA daily dose of 10 mg melatonin shows a slowly developing antioxidant profile in patients with arthritis and increases the concentrations of some inflammatory indicators, but these effects are not associated with any change of proinflammatory cytokine concentrations or clinical symptoms.
Cardiovascular toxicity due to metoprolol poisoning in a patient with coronary artery disease
Authors: Unverir Pinar , Topacoglu Hakan , Bozkurt Selim , Kaynak Firat 
Published: May 2007

What is already known about this subject• Poisoning with β‐blockers can result in cardiovascular and central nervous system effects.• Although much has been reported about metoprolol poisoning's cardiovascular complications, little attention has been paid to acute myocardial infarction (AMI) accompanied by elevated cardiac markers.What this study adds• This case report demonstrates for the first time an association of metoprolol poisoning with acute myocardial infarction in a patient with a previous history of coronary artery disease.• Metoprolol poisoning can induce acute myocardial reinfarction in patients with prior AMI or known coronary artery disease.• In other words, metoprolol overdose can trigger myocardial ischaemia and dysrhythmia in patients with coronary artery disease.AimTo demonstrate that β‐blocker poisoning results in cardiovascular and central nervous system findings.MethodsA 56‐year‐old woman was brought to the emergency department, having been admitted to hospital with 1500 mg of metoprolol ingestion 2 h previously. She had undergone percutanerous transluminal coronary angioplasty and stenting because of acute myocardial infarction (AMI). Her ECG revealed ST segment elevation in inferior leads and junctional dysrhythmia. Her clinical symptoms relieved after pacing and hospitalization and she was discharged.ResultsOur patient demonstrated findings of AMI with hypotension and bradycardia that appeared to result from metoprolol poisoning. Although one patient has been reported to have AMI associated with metoprolol poisoning, our patient is unique with her ECG changes and elevated cardiac markers: this is the first time that AMI characterized by elevated cardiac markers associated with metoprolol toxicity has been reported.ConclusionsEmergency physicians should bear in mind that AMI can accompany the presentation of metoprolol overdose in those with coronary artery disease. In other words, metoprolol poisoning can trigger myocardial ischaemia and dysrhythmia in those with coronary artery disease.
Daily ocean monitoring since the 1860s shows record warming of northern European seas
Authors: MACKENZIE BRIAN R. , SCHIEDEK DORIS 
Published: May 2007

AbstractOcean temperatures in most parts of the world are increasing and are expected to continue to rise during the 21st century. A major challenge to ecologists and marine resource managers is to understand and predict how these global changes will affect species and ecosystems at local scales where temperature more directly affects biological responses and species interactions. Here, we investigate historical variability in regional sea surface temperature in two large heavily exploited marine ecosystems and compare these variations with expected rates of temperature change for the 21st century. We use four of the world's longest calibrated daily time series to show that trends in surface temperatures in the North and Baltic Seas now exceed those at any time since instrumented measurements began in 1861 and 1880. Temperatures in summer since 1985 have increased at nearly triple the global warming rate, which is expected to occur during the 21st century and summer temperatures have risen two to five times faster than those in other seasons. These warm temperatures and rates of change are due partly to an increase in the frequency of extremely warm years. The recent warming event is exceeding the ability of local species to adapt and is consequently leading to major changes in the structure, function and services of these ecosystems.
A geographic mosaic of passive dispersal: population structure in the endemic Hawaiian amber snail Succinea caduca (Mighels, 1845)
Authors: HOLLAND BRENDEN S. , COWIE ROBERT H. 
Published: May 2007

AbstractWe used 276 cytochrome c oxidase subunit I (COI, 645 bp) and a subset of 84 16S large ribosomal subunit (16S, 451 bp) sequences to evaluate geographic patterns of genetic variation in 24 populations of the endemic Hawaiian land snail Succinea caduca spanning its range on six islands. Haplotype networks, gene tree topologies, pairwise molecular divergence and FST matrices suggest substantial geographic genetic structuring and complex dispersal patterns. Low nucleotide diversity and low pairwise molecular divergence values within populations coupled with higher between population values suggest multiple founder events. High overall haplotype diversity suggests diversification involving rare interpopulation dispersal, fragmentation by historical lava flows and variation in habitat structure. Within‐island rather than between‐island population comparisons accounted for the majority of molecular variance. Although 98% of 153 COI haplotypes were private by population, a Mantel test showed no evidence for isolation by distance. Mismatch distributions and population partitioning patterns suggest that genetic fragmentation has been driven by punctuated, passive dispersal of groups of closely related haplotypes that subsequently expanded and persisted in isolation for long periods (average > 2 million years ago), and that Pleistocene island connections may have been important in enhancing gene flow. Historical availability of mesic coastal habitat, together with effective dispersal may explain the long‐term persistence and unusual multi‐island distribution of this species, contrasting with the single‐island endemism of much of the Hawaiian biota.
Cardiolipin promotes polar localization of osmosensory transporter ProP in Escherichia coli
Authors: Romantsov Tatyana , Helbig Stephan , Culham Doreen E. , Gill Chad , Stalker Leanne , Wood Janet M. 
Published: May 2007

SummaryThe osmolality required to activate osmosensory transporter ProP and the proportion of cardiolipin (CL) among the phospholipids of Escherichia coli rise with growth medium osmolality. Most CL synthesis has been attributed to the cls gene product. Transcription of cls increased with osmolality. The proportion of CL was low and osmolality‐independent in cls– bacteria. It increased more dramatically on the transition to stationary phase in cls– than cls+ bacteria. Thus, Cls is responsible for osmoregulated CL synthesis and other enzymes may contribute to CL accumulation during stationary phase. The proportion of phosphatidylglycerol (PG) was elevated and it increased with medium osmolality in cls– bacteria. A cls defect impaired growth of E. coli on solid and in liquid media at low and, more strongly, at high osmolality. Bacteria cultured at high osmolality without osmoprotectant were shorter and rounder than those cultured at low osmolality or with glycine betaine. Fluorescence microscopy showed that CL and ProP colocalize at the poles and near the septa of dividing E. coli cells. The polar localization of ProP was independent of its expression level but correlated with the proportion and polar localization of CL. Association with CL (and not PG) may be required for polar ProP localization.