bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unzipping DNA from the condensed globule state—Effects of unraveling
Authors: Lam Pui‐Man , Levy J. C. 
Published: May 2005

AbstractWe have studied theoretically the unzipping of a double‐stranded DNA from a condensed globule state by an external force. At constant force, we found that the double‐stranded DNA unzips an at critical force Fc and the number of unzipped monomers M goes as M ∼ (Fc − F)−3, for both the homogeneous and heterogeneous double‐stranded DNA sequence. This is different from the case of unzipping from an extended coil state in which the number of unzipped monomers M goes as M ∼ (Fc − F)−χ, where the exponent χ is either 1 or 2 depending on whether the double‐stranded DNA sequence is homogeneous or heterogeneous, respectively. In the case of unzipping at constant extension, we found that for a double‐stranded DNA with a very large number N of base pairs, the force remains almost constant as a function of the extension, before the unraveling transition, at which the force drops abruptly to zero. Right at the unraveling transition, the number of base pairs remaining in the condensed globule state is still very large and goes as N3/4, in agreement with theoretical predictions of the unraveling transition of polymers stretched by an external force. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 287–291, 2005This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Minimally invasive transthoracotomy–transphrenotomy for concurrent hepatic and pulmonary hydatid disease
Authors: Lone G N , Bhat M A , Ali N , Ahangar A G , Dar A M , Sana I 
Published: May 2005

Abstract

Background
Combined liver and lung hydatid cysts are rare, but pose a challenge in terms of accessibility. The objective of the study was to find an alternative approach to conventional two-stage posterolateral thoracotomy and laparotomy or single-stage extensive thoracolaparotomy.

Methods
Twenty-five patients with right lung and liver hydatid disease underwent single-stage anterior minithoracotomy and phrenotomy. Primary diagnostic tools were chest radiography, ultrasonography and serology. The preferred mode of management of hydatid cysts was enucleation and partial or total capitonnage.

Results
Thirty-six (13·5 per cent) of 267 patients had concurrent hepatic and pulmonary hydatid cysts. Among the 25 patients who had anterior minithoracotomy and phrenotomy the male : female ratio was 2 : 1. Mean operating time was 75 min. Morbidity was negligible and postoperative recovery was prompt. All of the patients survived. The mean hospital stay was 5·2 days. Overall observations were encouraging.

Conclusion
This minimally invasive approach is associated with less morbidity and better cosmesis than conventional procedures. It represents an excellent alternative to other procedures in selected patients.
Population-based study of short- and long-term survival from colorectal cancer in Denmark, 1977–1999
Authors: Iversen L H , Pedersen L , Riis A , Friis S , Laurberg S , Sørensen H T 
Published: May 2005

AbstractBackgroundSurvival rates for patients with colorectal cancer have been lower in Denmark than in other European countries. The aim of this study was to examine temporal trends in relative survival from colorectal cancer between 1977 and 1999.MethodsAll patients diagnosed with colorectal cancer between 1977 and 1999 were identified using the nationwide population-based Danish Cancer Registry. Patients were linked with the Danish Central Population Registry to obtain data on survival to December 2002, and to select ten population controls per patient.ResultsA total of 69 562 patients with colorectal cancer were identified, of whom 49·2 per cent were men. Six-month relative survival after diagnosis increased from 69·7 per cent in 1977–1982 to 77·7 per cent in 1995–1999. Five-year relative survival rates increased from 37·8 to 46·8 per cent respectively. Women had slightly higher 5-year relative survival than men throughout the study period. Rectal tumours were associated with better survival than colonic tumours until 2 years after diagnosis, after which tumour location had no impact on survival.ConclusionRelative survival of patients with colorectal cancer has improved in Denmark between 1977 and 1999, most probably reflecting better management of the disease.
Cardiac troponin I predicts outcome after ruptured abdominal aortic aneurysm repair
Authors: Tambyraja A L , Dawson A R W , Murie J A , Chalmers R T A 
Published: May 2005

Abstract

Background
Cardiac troponin I (cTnI) is a highly sensitive and specific marker for myocardial injury that predicts mortality in patients with acute coronary syndromes. This study examined the relationship between perioperative cTnI levels and clinical outcome in patients with ruptured abdominal aortic aneurysm (AAA).

Methods
Consecutive patients who underwent operative repair of a ruptured AAA over a 22-month interval and survived for more than 24 h were entered into a prospective observational cohort study. Levels of cTnI were measured immediately before, and at 24 and 48 h after surgery, and related to clinical outcome.

Results
Of 62 patients who underwent attempted operative repair of ruptured AAA, 50 (81 per cent) survived for more than 24 h and were included in this study. Twenty-three (46 per cent) of the 50 had a detectable cTnI level at one or more time points during the first 48 h. Of these, 11 patients had clinical or electrocardiographic evidence of an acute cardiac event and 12 did not; five patients in each of these two groups died. Of 27 patients with no increase in cTnI in the first 48 h, only three died (P = 0·031 and P = 0·043 respectively, relative to the groups with detectable cTnI).

Conclusion
Approximately half of patients who survived repair of ruptured AAA for more than 24 h sustained a detectable myocardial injury within the first 48 h. A perioperative increase in the level of cTnI, with or without clinically apparent cardiac dysfunction, was associated with postoperative death.
Diatom/Copepod Interactions in Plankton: The Indirect Chemical Defense of Unicellular Algae
Authors: Pohnert Georg 
Published: May 2005

AbstractNumerous coexisting species can be observed in the open oceans. This includes the complex community of the plankton, which comprises all free floating organisms in the sea. Traditionally, nutrient limitation, competition, predation, and abiotic factors have been assumed to shape the community structure in this environment. Only in recent years has the idea arisen that chemical signals and chemical defense can influence species interactions in the plankton as well. Key players at the base of the marine food web are diatoms (unicellular algae with silicified cell walls) and their main predators, the herbivorous copepods. It was assumed that diatoms represent a generally good food source for the grazers but recent work indicates that some species use chemical defenses. Secondary metabolites, released by these algae immediately after wounding, are targeted not against the predators themselves but rather at interfering with their reproductive success. This strategy allows diatoms to reduce the grazer population, thereby influencing the marine food web. This review addresses the chemical ecology of the defensive oxylipins formed by diatoms and the question of how these metabolites can act in such a dilute environment. Aspects of biosynthesis, bioassays, and the possible implications of such a chemical defense for the plankton community structure are also discussed.
PIGA (N,N‐Di‐n‐butyl‐5‐chloro‐2‐(4‐chlorophenyl)indol‐3‐ylglyoxylamide), a New Mitochondrial Benzodiazepine‐Receptor Ligand, Induces Apoptosis in C6 glioma Cells
Authors: Chelli Beatrice , Rossi Leonardo , Da Pozzo Eleonora , Costa Barbara , Spinetti Francesca , Rechichi Mariarosa , Salvetti Alessandra , Lena Annalisa , Simorini Francesca , Vanacore Renato , Scatena Fabrizio , Da Settimo Federico , Gremigni Vittorio , Martini Claudia 
Published: May 2005

AbstractMitochondrial benzodiazepine‐receptor (mBzR) ligands constitute a heterogeneous class of compounds that show a pleiotropic spectrum of effects within the cells, including the modulation of apoptosis. In this paper, a novel synthetic 2‐phenylindol‐3‐ylglyoxylamide derivative, N,N‐di‐n‐butyl‐5‐chloro‐2‐(4‐chlorophenyl)indol‐3‐ylglyoxylamide (PIGA), which shows high affinity and selectivity for the mBzR, is demonstrated to induce apoptosis in rat C6 glioma cells. PIGA was able to dissipate mitochondrial transmembrane potential (ΔΨm) and to cause a significant cytosolic accumulation of cytochrome c. Moreover, typical features of apoptotic cell death, such as caspase‐3 activation and DNA fragmentation, were also detected in PIGA‐treated cells. Our data expand the knowledge on mBzR ligand‐mediated apoptosis and suggest PIGA as a novel proapoptotic compound with therapeutic potential against glial tumours, in which apoptosis resistance has been reported to be involved in carcinogenesis.
New Inhibitors of the Tat–TAR RNA Interaction Found with a “Fuzzy” Pharmacophore Model
Authors: Renner Steffen , Ludwig Verena , Boden Oliver , Scheffer Ute , Göbel Michael , Schneider Gisbert 
Published: May 2005

AbstractTAR RNA is a potential target for AIDS therapy. Ligand‐based virtual screening was performed to retrieve novel scaffolds for RNA‐binding molecules capable of inhibiting the Tat–TAR interaction, which is essential for HIV replication. We used a “fuzzy” pharmacophore approach (SQUID) and an alignment‐free pharmacophore method (CATS3D) to carry out virtual screening of a vendor database of small molecules and to perform “scaffold‐hopping”. A small subset of 19 candidate molecules were experimentally tested for TAR RNA binding in a fluorescence resonance energy transfer (FRET) assay. Both methods retrieved molecules that exhibited activities comparable to those of the reference molecules acetylpromazine and chlorpromazine, with the best molecule showing ten times better binding behavior (IC50=46 μM). The hits had molecular scaffolds different from those of the reference molecules.
Examples of Peptide–Peptoid Hybrid Serine Protease Inhibitors Based on the Trypsin Inhibitor SFTI‐1 with Complete Protease Resistance at the P1P1′ Reactive Site
Authors: Stawikowski Maciej , Stawikowska Roma , Jaśkiewicz Anna , Zabłotna Ewa , Rolka Krzysztof 
Published: May 2005

AbstractResearch in the field of protease inhibitors is focused on obtaining potent, specific and protease‐resistant inhibitors. To our knowledge, there are no reports in the literature that consider the application of N‐substituted glycine residues (peptoid monomers) for the design of peptidomimetic protease inhibitors. We hereby present the chemical synthesis and kinetic properties of two new analogues of the trypsin inhibitor SFTI‐1 modified at the P1 position. Substitution of Lys5 in SFTI‐1 by N‐(4‐aminobutyl)‐glycine and N‐benzylglycine, which mimic Lys and Phe, respectively, made these analogues completely protease‐resistant at their P1P1′ reactive sites. The analogues synthesised appeared to be potent inhibitors of bovine β‐trypsin and α‐chymotrypsin. These noncovalent, competitive and selective peptide–peptoid hybrid (peptomeric) inhibitors might open the way to targeting unwanted proteolysis.
Lewis Acidity/Basicity of π‐Electron Systems: Theoretical Study of a Molecular Interaction between a π System and a Lewis Acid/Base
Authors: Kawahara Shun‐ichi , Tsuzuki Seiji , Uchimaru Tadafumi 
Published: May 2005

AbstractMolecular interactions between π systems having different π‐electron character (benzene, hexafluorobenzene, and borazine), and a Lewis acid/base (borane and ammonia) were theoretically studied. An attractive interaction between benzene, the electron‐rich π system, and borane was observed. On the other hand, repulsive interactions between benzene and ammonia was observed when the lone pair of nitrogen points toward the benzene ring. In contrast, an attractive interaction between hexafluorobenzene, an electron‐deficient π system, and ammonia was observed. Unexpectedly, a weak attractive interaction between hexafluorobenzene and borane was also observed. Borazine shows an interaction both to borane and ammonia. The attraction between the nitrogen atom of borazine and borane was larger than that between the boron atom of borazine and ammonia.
Highly Hydrated Cations: Deficiency, Mobility, and Coordination of Water in Crystalline Nonahydrated Scandium(III), Yttrium(III), and Lanthanoid(III) Trifluoromethanesulfonates
Authors: Abbasi Alireza , Lindqvist‐Reis Patric , Eriksson Lars , Sandström Dick , Lidin Sven , Persson Ingmar , Sandström Magnus 
Published: May 2005

AbstractTrivalent lanthanide‐like metal ions coordinate nine water oxygen atoms, which form a tricapped trigonal prism in a large number of crystalline hydrates. Water deficiency, randomly distributed over the capping positions, was found for the smallest metal ions in the isomorphous nonahydrated trifluoromethanesulfonates, [M(H2O)n](CF3SO3)3, in which M=ScIII, LuIII, YbIII, TmIII or ErIII. The hydration number n increases (n=8.0(1), 8.4(1), 8.7(1), 8.8(1) and 8.96(5), respectively) with increasing ionic size. Deuterium (2H) solid‐state NMR spectroscopy revealed fast positional exchange between the coordinated capping and prism water molecules; this exchange started at temperatures higher than about 280 K for lutetium(III) and below 268 K for scandium(III). Similar positional exchange for the fully nonahydrated yttrium(III) and lanthanum(III) compounds started at higher temperatures, over about 330 and 360 K, respectively. An exchange mechanism is proposed that can exchange equatorial and capping water molecules within the restrictions of the crystal lattice, even for fully hydrated lanthanoid(III) ions. Phase transitions occurred for all the water‐deficient compounds at ≈185 K. The hydrated scandium(III) trifluoromethanesulfonate transforms reversibly (ΔH°=−0.80(1) kJ mol−1 on cooling) to a trigonal unit cell that is almost nine times larger, with the scandium ion surrounded by seven fully occupied and two partly occupied oxygen atom positions in a distorted capped trigonal prism. The hydrogen bonding to the trifluoromethanesulfonate anions stabilises the trigonal prism of water ligands, even for the crowded hydration sphere of the smallest metal ions in the series. Implications for the Lewis acid catalytic activity of the hydrated scandium(III) and lanthanoid(III) trifluoromethanesulfonates for organic syntheses performed in aqueous media are discussed.
Squamous cell carcinoma antigen‐immunoglobulin M complexes as novel biomarkers for hepatocellular carcinoma
Authors: Beneduce Luca , Castaldi Francesco , Marino Maria , Quarta Santina , Ruvoletto Mariagrazia , Benvegnù Luisa , Calabrese Fiorella , Gatta Angelo , Pontisso Patrizia , Fassina Giorgio 
Published: May 2005

AbstractBACKGROUNDEarly detection of hepatocellular carcinoma (HCC), one of the most common and deadly tumors worldwide, still is difficult due to the lack of adequate biomarkers that show high sensitivity and specificity. The authors recently demonstrated that squamous cell carcinoma antigen (SCCA) variants were overexpressed remarkably in all surgically resected HCCs.METHODSFor the current study, the authors assessed the presence of SCCA, as a free form and complexed with immunoglobulins, in serum from patients with HCC, cirrhosis, and chronic hepatitis and from healthy control participants and compared SCCA measurement with the measurement of α‐fetoprotein (AFP) levels.RESULTSCirculating immune complexes (ICs) composed by SCCA and immunoglobulin M (IgM) IC (SCCA‐IgM IC) were undetectable (< 120 arbitrary units [AU]/mL) in serum from a healthy control population (0 of 73 controls); however, 35 of 50 patients with HCC (70%) were reactive for SCCA‐IgM IC independent of etiology (mean ± standard deviation [SD], 2568.5 ± 6797.3 AU/mL). No correlation was found with AFP levels, which were elevated significantly in only 21 of 50 patients with HCC (42%). By using an AFP cut‐off value of 20 ng/mL, 96% of patients with HCC were positive for at least 1 marker. Among cirrhotic patients, the presence of circulating SCCA‐IgM IC was displayed in 13 of 50 patients (26%), but at lower levels compared with the patients who had HCC (mean ± SD, 147.5 ± 348.3 AU/mL; P < 0.01; Student t test), whereas 9 of 50 patients with chronic hepatitis (18%) were reactive (mean ± SD, 39.5 ± 89.7 AU/mL). No significant presence of free SCCA, free anti‐SCCA variants IgG or IgM, or SCCA‐IgG IC was found.CONCLUSIONSThe study results indicated that SCCA‐IgM ICs represent novel serologic biomarkers, which, alone or in combination with AFP, can increase the sensitivity for diagnosing HCC significantly. Cancer 2005. © 2005 American Cancer Society.
A phase II study of bortezomib in the treatment of metastatic malignant melanoma
Authors: Markovic Svetomir N. , Geyer Susan M. , Dawkins Fitzroy , Sharfman William , Albertini Mark , Maples William , Fracasso Paula M. , Fitch Tom , LoRusso Patricia , Adjei Alex A. , Erlichman Charles 
Published: May 2005

AbstractBACKGROUNDBortezomib is a proteasome inhibitor with manageable clinical toxicity and laboratory evidence of anti‐melanoma activity. Therefore, it was considered for clinical testing in patients with metastatic melanoma.METHODSPatients with metastatic melanoma and adequate hematologic, renal, and hepatic function were treated with bortezomib (a 1.5‐mg/m2 intravenous bolus twice weekly for 2 of every 3 weeks). Eligible patients were age ≥ 18 years with an Eastern Cooperative Oncology Group performance status of 0–1. The primary goal of the current study was to evaluate the 18‐week disease progression‐free survival rate and tolerability of bortezomib in these patients.RESULTSThe current study was intended to treat 45 patients. It was closed at the planned interim analysis due to early evidence of insufficient clinical efficacy. Twenty‐seven patients with a median age of 56 years (range, 32–77 years)were accrued. There were no major clinical responses to treatment. Only 6 patients (22%) achieved stable disease. Of these 6 patients, 4 were still stable after 4 cycles of treatment, but were removed from the study due to toxicity. The median time to disease progression was 1.5 months (95% confidence interval [95% CI], 1.4–1.6) with a median overall survival of 14.5 months (95% CI, 9–22). Having failed bortezomib, most patients proceeded to other clinical trials. Twenty‐six patients were evaluable for toxicity. One patient was removed from the study for other reasons and could not return for the cycle evaluation and thus was never evaluated. Of the 26 patients, no Grade 4/5 treatment‐related toxicities (using the National Cancer Institute Common Toxicity Criteria [version 2.0]) were reported. Eleven patients (42%) had Grade 3 toxicities (believed to be at least possibly related to treatment), including sensory neuropathy, thrombocytopenia, constipation, fatigue, ileus, abdominal pain, and infection without neutropenia. The median number of treatment cycles patients received was two (range, one to six treatment cycles). Two patients (7%) had 1 dose delay and 6 patients (22%) had dose reductions during 1 treatment cycle due to adverse events.CONCLUSIONSSingle‐agent bortezomib, administered twice weekly × 2 weeks, every 3 weeks at a dose of 1.5 mg/m2, was not found to be effective in the treatment of patients with metastatic melanoma. Cancer 2005. © 2005 American Cancer Society.
Topographic activation of the medial entorhinal cortex by presubicular commissural projections
Authors: Bartesaghi Renata , Di Maio Vito , Gessi Tiziana 
Published: May 2005

AbstractPrevious investigations have shown that presubicular commissural fibers traveling in the caudal part of the dorsal hippocampal commissure (PSD) selectively activated the dorsalmost portion of the entorhinal cortex (EC), where they discharged perforant path neurons to the dorsal dentate gyrus. The dentate activation was followed by that of the dorsal hippocampus. The aim of the present study was to ascertain whether presubiculum commissural projections traveling in the PSD can also activate ventral levels of the EC and, if so, whether this activation is followed by that of the dentate gyrus‐hippocampal system in the ventral hippocampus. The experiments were carried out in adult, anesthetized guinea pigs by field potential analysis. The results showed that presubicular fibers traveling at different PSD loci selectively activated specific EC portions, with caudal fibers activating only the dorsal EC and more rostral fibers activating ventral EC points. The region activated by PSD projections corresponded to the medial EC. Current source‐density (CSD) analysis revealed that at both dorsal and ventral EC levels excitatory synaptic potentials followed by neuron discharge were generated in layer II, site of origin of the perforant path to the dentate gyrus. Activation of either dorsal or ventral levels of the EC was followed by activation of the dentate gyrus‐hippocampal system in corresponding hippocampal segments. The results provide physiological evidence that the commissural presubicular projections activate the EC in a topographic manner. The massive activation of perforant path neurons at all EC levels suggests that presubicular signals may strongly influence the functions played by the EC‐dentate‐hippocampal system. J. Comp. Neurol. 487:283–299, 2005. © 2005 Wiley‐Liss, Inc.
Anatomical abnormalities in dopaminoceptive regions of the cerebral cortex of dopamine D1 receptor mutant mice
Authors: Stanwood Gregg D. , Parlaman Joshua P. , Levitt Pat 
Published: May 2005

AbstractAlteration of dopamine neurotransmission during development can induce specific changes in neuronal structure and function. Here, we report specific morphological and neurochemical changes of projection neurons and interneurons of the medial frontal cortex of the dopamine D1 receptor null mouse. Using immunostaining of cytoskeletal proteins and a crossbred D1 receptor null:YFP transgenic reporter line, we demonstrate that the apical dendrites of pyramidal cells are abnormally organized in the prefrontal and anterior cingulate cortices of mice lacking the D1 receptor. Neuronal processes exhibit a decrease in bundling and an increase in irregular, tortuous patterning as they weave a course towards the pial surface. In addition, there is increased parvalbumin staining of the dendrites of cortical interneurons in D1 receptor null mice. Both pyramidal and interneuron alterations are evident by the early postnatal period and persist into adulthood. The alterations show regional specificity, in that dendritic profiles of projection neurons and interneurons in somatosensory and visual cortices develop normally. The abnormalities are reminiscent of those induced by prenatal exposure to cocaine in rabbits, an insult which has been shown to produce an attenuation of D1 receptor‐mediated responses through Gsα. These results suggest that loss of D1 receptor‐mediated signaling during development produces permanent alterations in the cellular organization of specific cortical areas involved in attention, cognition, and emotion. Pharmacological and behavioral studies in the D1 null mouse should be interpreted in the context of possible altered circuitry, given the presence of these developmental defects in the organization of dopaminoceptive regions of the cerebral cortex. J. Comp. Neurol. 487:270–282, 2005. © 2005 Wiley‐Liss, Inc.