bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solving and analyzing side-chain positioning problems using linear and integer programming
Authors: Kingsford Carleton L. , Chazelle Bernard , Singh Mona 
Published: November 2004

Abstract
Motivation: Side-chain positioning is a central component of homology modeling and protein design. In a common formulation of the problem, the backbone is fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optimized. It is NP-complete to find even a reasonable approximate solution to this problem. We seek to put this hardness result into practical context.
Results: We present an integer linear programming (ILP) formulation of side-chain positioning that allows us to tackle large problem sizes. We relax the integrality constraint to give a polynomial-time linear programming (LP) heuristic. We apply LP to position side chains on native and homologous backbones and to choose side chains for protein design. Surprisingly, when positioning side chains on native and homologous backbones, optimal solutions using a simple, biologically relevant energy function can usually be found using LP. On the other hand, the design problem often cannot be solved using LP directly; however, optimal solutions for large instances can still be found using the computationally more expensive ILP procedure. While different energy functions also affect the difficulty of the problem, the LP/ILP approach is able to find optimal solutions. Our analysis is the first large-scale demonstration that LP-based approaches are highly effective in finding optimal (and successive near-optimal) solutions for the side-chain positioning problem.
Availability: The source code for generating the ILP given a file of pairwise energies between rotamers is available online at http://compbio.cs.princeton.edu/scplp
Contact: msingh@cs.princeton.edu
3‐O‐Methylfunicone, a secondary metabolite produced by Penicillium pinophilum, induces growth arrest and apoptosis in HeLa cells
Authors: Buommino E. , Nicoletti R. , Gaeta G. M. , Orlando M. , Ciavatta M. L. , Baroni A. , Tufano M. A. 
Published: November 2004

Abstract.  3‐O‐Methylfunicone (OMF) is a secondary metabolite produced by the soil fungus Penicillium pinophilum which has cytostatic properties. The aim of this study was to investigate the mechanisms by which such properties are exerted, with special reference to any anti‐proliferative and apoptotic potential, on HeLa cells. OMF treatment caused about 44% inhibition of cell growth after 24 h, and modifications in the tubulin fibre organization. In addition, a significant increase in p21 mRNA expression and a decrease in cyclin D1 and Cdk4 mRNA expression resulted at the same time. Apoptosis induction was demonstrated by the annexin V assay, cytofluorimetric analysis of the DNA content of the sub‐G1 fraction and DNA laddering. Taken together, our data showed that the compound inhibits proliferation of HeLa cells by several mechanisms, such as disruption of tubulin fibres, cell cycle arrest and apoptosis induction. The capacity of the compound to affect the cell cycle and to modulate apoptosis is indicative of a potential for the development of a new agent for cancer chemotherapy.
Quality of life and symptoms among older people living at home
Authors: Hellström Ylva , Persson Gunnel , Hallberg Ingalill R. 
Published: November 2004

Aim.  This paper reports a study comparing the socio‐demographic data, quality of life (QoL) and symptoms of older people living at home with and without help.Background.  Despite growing numbers of older people worldwide, little is know about the differences between older people receiving help to live at home and those not receiving this, especially as regards QoL and symptoms. Not only symptoms but also dependency on others per se may reduce older people's QoL. From a nursing perspective, knowledge about such issues is important because the impact of symptoms may be reducible, even when diseases cannot be cured.Method.  A postal questionnaire was sent to an age‐stratified random sample of 1866 people aged 75 years or over. Of the respondents (n = 1248) 448 received help and 793 did not.Results.  The group receiving help had a significantly higher age, more women, more people widowed and living alone, more children, a higher number of self‐reported diseases and symptoms, greater inability to remain alone at home and lower QoL. Loneliness, depressed mood and abdominal pain were significantly related to low QoL in both groups. Living alone, not being able to remain alone at home without help, and fatigue were also predictive of low QoL among those receiving help, and number of diseases and sleep problems in those without.Conclusion.  Receiving help with daily living seems to be significantly related to low QoL and goes along with a high number of symptoms that need to be considered in nursing care. Through regular visits, systematic assessment and intervention, especially focusing on older people's symptoms, nurses may contribute to improved QoL for this section of the population.
Host and non‐host pathogens elicit different jasmonate/ethylene responses in Arabidopsis
Authors: Zimmerli Laurent , Stein Mónica , Lipka Volker , Schulze‐Lefert Paul , Somerville Shauna 
Published: November 2004

Summary Arabidopsis does not support the growth and asexual reproduction of the barley pathogen, Blumeria graminis f. sp. hordei Bgh). A majority of germlings fail to penetrate the epidermal cell wall and papillae. To gain additional insight into this interaction, we determined whether the salicylic acid (SA) or jasmonate (JA)/ethylene (ET) defence pathways played a role in blocking barley powdery mildew infections. Only the eds1 mutant and NahG transgenics supported a modest increase in penetration success by the barley powdery mildew. We also compared the global gene expression patterns of Arabidopsis inoculated with the non‐host barley powdery mildew to those inoculated with a virulent, host powdery mildew, Erysiphe cichoracearum. Genes repressed by inoculations with non‐host and host powdery mildews relative to non‐inoculated control plants accounted for two‐thirds of the differentially expressed genes. A majority of these genes encoded components of photosynthesis and general metabolism. Consistent with this observation, Arabidopsis growth was inhibited following inoculation with Bgh, suggesting a shift in resource allocation from growth to defence. A number of defence‐associated genes were induced during both interactions. These genes likely are components of basal defence responses, which do not effectively block host powdery mildew infections. In addition, genes encoding defensins, anti‐microbial peptides whose expression is under the control of the JA/ET signalling pathway, were induced exclusively by non‐host pathogens. Ectopic activation of JA/ET signalling protected Arabidopsis against two biotrophic host pathogens. Taken together, these data suggest that biotrophic host pathogens must either suppress or fail to elicit the JA/ET signal transduction pathway.
The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome
Authors: Duroux Meg , Houben Andreas , Růžička Kamil , Friml Jiří , Grasser Klaus D. 
Published: November 2004

SummaryThe packaging of the genomic DNA into chromatin in the cell nucleus requires machineries that facilitate DNA‐dependent processes such as transcription in the presence of repressive chromatin structures. Using co‐immunoprecipitation we have identified in Arabidopsis thaliana cells the FAcilitates Chromatin Transcription (FACT) complex, consisting of the 120‐kDa Spt16 and the 71‐kDa SSRP1 proteins. Indirect immunofluorecence analyses revealed that both FACT subunits co‐localize to nuclei of the majority of cell types in embryos, shoots and roots, whereas FACT is not present in terminally differentiated cells such as mature trichoblasts or cells of the root cap. In the nucleus, Spt16 and SSRP1 are found in the cytologically defined euchromatin of interphase cells independent of the status of DNA replication, but the proteins are not associated with heterochromatic chromocentres and condensed mitotic chromosomes. FACT can be detected by chromatin immunoprecipitation over the entire transcribed region (5′‐UTR, coding sequence, 3′‐UTR) of actively transcribed genes, whereas it does not occur at transcriptionally inactive heterochromatic regions and intergenic regions. FACT localizes to inducible genes only after induction of transcription, and the association of the complex with the genes correlates with the level of transcription. Collectively, these results indicate that FACT assists transcription elongation through plant chromatin.
Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives
Authors: Rana Debashis , van den Boogaart Tom , O'Neill Carmel M. , Hynes Llewelyn , Bent Elisabeth , Macpherson Lee , Park Jee Young , Lim Yong Pyo , Bancroft Ian 
Published: November 2004

SummaryThe cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10 000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species‐specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.
ACC synthase expression regulates leaf performance and drought tolerance in maize
Authors: Young Todd E. , Meeley Robert B. , Gallie Daniel R. 
Published: November 2004

SummaryEthylene regulates entry into several types of plant developmental cell death and senescence programs besides mediating plant responses to biotic and abiotic stress. The response of cereals to conditions of drought includes loss of leaf function and premature onset of senescence in older leaves. In this study, ACC synthase (ACS) mutants, affecting the first step in ethylene biosynthesis, were isolated in maize and their effect on leaf function examined. Loss of ZmACS6 expression resulted in delayed leaf senescence under normal growth conditions and inhibited drought‐induced senescence. Zmacs6 leaves continued to be photosynthetically active under both conditions indicating that leaf function was maintained. The delayed senescence phenotype associated with loss of ZmACS6 expression was complemented by exogenous ACC. Surprisingly, elevated levels of foliar chlorophyll, Rubisco, and soluble protein as well as improved leaf performance was observed for all Zmasc6 leaves, including young and fully expanded leaves which were far from initiating senescence. These observations suggest that ethylene may serve to regulate leaf performance throughout its lifespan as well as to determine the onset of natural senescence and mediate drought‐induced senescence.
Citation patterns in tropical medicine journals
Authors: Schoonbaert Dirk 
Published: November 2004

SummarySelections of most important journals in the field of tropical medicine have previously been identified with the help of resources such as bibliographical and citation databases. This article uses ISI's Journal Citation Reports (JSR) for 2002 to analyse the citation characteristics of the Tropical Medicine category. According to these data, this small but diverse group of 12 journals bestows some 40% more citations than it receives. Its six typical core journals tend to cite one another heavily, but they also refer a lot to multidisciplinary science and general medicine journals, and to infectious diseases and parasitology journals. Looking at the sources from which JCR's tropical medicine journals derive their citations, it is clear that in this reverse direction, the specialty's literature is still more concentrated. Apart from the typical core, this JCR category also contains a number of journals with more idiosyncratic citing patterns, focused on specialties such as paediatrics, a single disease (leprosy) and a representative of Latin American and Francophone biomedical science each. Implications of concentrated citedness and language biases are discussed briefly. This paper features a selection of bibliometric parameters relating to the tropical medicine journals and lists of the 80 journals most citing and cited by them.
Is there an association between bacteriological drinking water quality and childhood diarrhoea in developing countries?
Authors: Jensen P. K. , Jayasinghe G. , van der Hoek W. , Cairncross S. , Dalsgaard A. 
Published: November 2004

SummaryTo investigate the association between bacteriological drinking water quality and incidence of diarrhoea, we conducted a 1‐year prospective study in the southern Punjab, Pakistan. Diarrhoea episodes, drinking water sources and drinking water quality were monitored weekly among children younger than 5 years in 200 households. We found no association between the incidence of childhood diarrhoea and the number of Escherichia coli in the drinking water sources (the public domain). A possible trend was seen relating the number of E. coli in the household storage containers (the domestic domain) and diarrhoea incidence, but this did not reach statistical significance. Faecal contamination levels in household water containers were generally high even when the source water was of good quality. Under conditions such as this, it is questionable whether public water treatment will have a significant impact on the incidence of endemic childhood diarrhoea.
Review of experience over four decades in the management of carotid body tumours
Authors: Lin Yongjie , Li Songqi , Poon Jensen Tung‐Chung , Hu Zuojun , Ye Caisheng , Lu Weiming , Chen Guorui , Wang Shenming 
Published: November 2004

Objective:  To review the experience of the management of carotid body tumours in a major vascular centre in mainland China.Patients and methods:  This was a retrospective review of 52 cases of carotid body tumour. There were 24 male and 28 female patients with an age range of 18–67 years; and 23 right‐sided, 24 left‐sided and five bilateral lesions. The modality of preoperative imaging was as follows: duplex scan and computed tomography in 40 cases, magnetic resonance imaging in 10 cases, carotid artery angiogram in 32 cases with selective embolization of the feeding vessel in 19. Operative treatment was carried out for 55 lesions and was summarized as follows: simple tumour excision for 44 lesions and en bloc tumour excision together with carotid bifurcation for 11 lesions; ICA reconstruction with interposition graft in three cases; and external to ICA anastomosis in two cases. Results:  There were no operative mortalities. Postoperative complications included two ischaemic strokes, one case of vagus nerve damage and one case of hypoglossal nerve damage. Conclusion:  Carotid body tumour is a rare neoplasm. Its special anatomical position imposes great difficulty during surgery. Adequate preoperative preparation and embolization of feeding arteries could reduce operative blood loss, improve tumour excision and preserve the ICA flow.
Feasibility of laparoscopic common bile duct exploration in a rural centre
Authors: Hemli Jonathan M. , Arnot Richard S. , Ashworth Jack J. , Curtin Austin M. , Simon Robert A. , Townend David M. 
Published: November 2004

Background:  Laparoscopic common bile duct exploration has emerged as a preferred option for the management of choledocholithiasis. The present study sought to review the feasibility of this technique in a rural centre.Methods:  A comprehensive retrospective review was undertaken of all patients who underwent surgical treatment of biliary calculi in Lismore, NSW (Australia), between January 1996 and December 2002.Results:  During the study period, 1567 consecutive patients underwent laparoscopic cholecystectomy, of whom 82 (5.2%) had choledocholithiasis identified at intraoperative cholangiography. A total of 86 laparoscopic common bile duct explorations were undertaken in these patients, 37 (43%) via a transcystic approach, and 49 (57%) via a laparoscopic choledochotomy. All common bile duct calculi were successfully removed in 78 cases, representing an overall duct clearance rate of 90.7%. Complications were noted in seven patients, a morbidity rate of 8.5%. Median operative time for the procedure over the study period was 173 min. Median hospital stay was 6 days for all patients.Conclusions:  Laparoscopic common bile duct exploration can be successfully undertaken in a rural setting by general surgeons who have appropriate laparoscopic experience, and should be the procedure of choice for the management of choledocholithiasis in these patients. It should not be restricted to specialized surgical departments in major referral centres.
Choledochal cyst in adults: aetiological considerations to intrahepatic involvement
Authors: Cheng Shih‐Ping , Yang Tsen‐Long , Jeng Kuo‐Shyang , Liu Chien‐Liang , Lee Jie‐Jen , Liu Tsang‐Pai 
Published: November 2004

Background:  Choledochal cysts are rare anomalies of the biliary tree and their presentation in adults is infrequent. The high incidence of associated anomalous pancreaticobiliary duct junction (APBDJ) has been well documented. However, the prevalence of APBDJ in different anatomic distribution of cysts has yet to be clarified.Methods:  A total 39 adult patients with choledochal cysts were consecutively enrolled: 22 patients had Todani type I cysts, 16 patients had type IVa cysts, and one patient had a type IVb cyst.Results:  No statistical differences were found in age, sex or manifestations. A higher frequency of associated APBDJ was identified in patients with type IVa cyst (100%) than those with type I cyst (P < 0.05). With a mean follow‐up of 7.2 years after cyst excision, three patients with type I choledochal cyst and four with type IVa cyst have had episodes of recurrent cholangitis, all accompanied with preoperatively diagnosed APBDJ.Conclusion:  Anomalous pancreaticobiliary duct junction has a close relationship with adult choledochal cysts, particularly type IVa. We propose the hypothesis that intrahepatic involvement results from progressive enzymatic destruction. Adult choledochal cysts in association with APBDJ, with or without intrahepatic component, should be carefully monitored.
Self‐Expression and Self‐Control
Authors: Schechtman Marya 
Published: November 2004

AbstractIt is often said that people are ‘not themselves’ when they are in situations which rob them of their self‐control. Strangely, these are also circumstances in which people are often said to be most fully themselves. This paper investigates the pictures of the self behind these two truisms, and the relation between them. Harry Frankfurt’s work represents the first truism, and standard objections to his work the second. Each of these approaches is found to capture one independent and widely employed picture of the self. The connection each draws between being oneself and flourishing, however, suggests a point of contact between them. This point of contact is used to develop a third view of being oneself which integrates the insights of the other two.
Carvedilol attenuates ischemia–reperfusion‐induced oxidative renal injury in rats
Authors: Singh Devinder , Chander Vikas , Chopra Kanwaljit 
Published: November 2004

AbstractThere is increasing evidence to suggest that toxic oxygen radicals play a role in the pathogenesis of ischemia/reperfusion (I/R) injury in the kidney. This study was designed to investigate the effects of carvedilol (CVD), an antihypertensive drug in I/R‐induced renal failure in rats. The protective effect of CVD against the damage inflicted by reactive oxygen species (ROS) during renal I/R was investigated in Sprague–Dawley rats using histopathological and biochemical parameters. In one set of experiments, animals were unilaterally nephrectomized, and subjected to 45 min of left renal pedicle occlusion and in another set both the renal pedicles were occluded for 45 min followed by 24 h of reperfusion. Carvedilol (2 mg/kg, i.p.) was administered twice, 30 min prior to ischemia and 12 h after the reperfusion period. At the end of the reperfusion period, rats were killed. Thiobarbituric acid‐reactive substances (TBARS), reduced glutathione (GSH) levels, catalase (CAT) and superoxide dismutase (SOD) activities were determined in renal tissue. Serum creatinine and blood urea nitrogen (BUN) concentrations were measured for the evaluation of renal function. Ischemic control animals demonstrated severe deterioration of renal function, renal morphology and a significant renal oxidative stress. Pretreatment of animals with CVD markedly attenuated renal dysfunction, morphological alterations, reduced elevated TBARS levels and restored the depleted renal antioxidant enzymes. The findings imply that ROS play a causal role in I/R‐induced renal injury and CVD exerts renoprotective effects probably by the radical scavenging and antioxidant activities.