bluuebunny/crossref_metadata_2025 huggingface dataset:
Interaction of polymorphisms in the genes encoding interleukin‐6 and estrogen receptor beta on the susceptibility to Parkinson's disease
Authors: Håkansson Anna , Westberg Lars , Nilsson Staffan , Buervenich Silvia , Carmine Andrea , Holmberg Björn , Sydow Olof , Olson Lars , Johnels Bo , Eriksson Elias , Nissbrandt Hans
Published: January 2005

The multifunctional cytokine interleukin‐6 (IL‐6) is involved in inflammatory processes in the central nervous system and increased levels of IL‐6 have been found in patients with Parkinson's disease (PD). It is known that estrogen inhibits the production of IL‐6, via action on estrogen receptors, thereby pointing to an important influence of estrogen on IL‐6. In a previous study, we reported an association between a G/A single nucleotide polymorphism (SNP) at position 1730 in the gene coding for estrogen receptor beta (ERbeta) and age of onset of PD. To investigate the influence of a G/C SNP at position 174 in the promoter of the IL‐6 gene, and the possible interaction of this SNP and the ERbeta G‐1730A SNP on the risk for PD, the G‐174C SNP was genotyped, by pyrosequencing, in 258 patients with PD and 308 controls. A significantly elevated frequency of the GG genotype of the IL‐6 SNP was found in the patient group and this was most obvious among patients with an early age of onset (≤50 years) of PD. When the GG genotypes of the IL‐6 and ERbeta SNPs were combined, the combination was much more robustly associated with PD, and especially with PD with an early age of onset, than respective GG genotype when analyzed separately. Our results indicate that the G‐174C SNP in the IL‐6 promoter may influence the risk for developing PD, particularly regarding early age of onset PD, and that the effect is modified by interaction of the G‐1730A SNP in the ERbeta gene. © 2004 Wiley‐Liss, Inc.
A family study of obsessive‐compulsive disorder with pediatric probands
Authors: Hanna Gregory L. , Himle Joseph A. , Curtis George C. , Gillespie Brenda W.
Published: January 2005

Obsessive‐compulsive disorder (OCD) is a heterogeneous disorder of unknown etiology. We examined the lifetime history of obsessions, compulsions, and OCD in the first‐ and second‐degree relatives of 35 pediatric probands with OCD and 17 controls with no psychiatric diagnosis. All available first‐degree relatives were directly interviewed blind to proband status with two semi‐structured interviews. Parents were also interviewed to systematically assess the family psychiatric history of first‐ and second‐degree relatives. Best‐estimate lifetime diagnoses were made using all available sources of information. Data were analyzed with logistic regression by the generalized estimating equation method and with robust Cox regression models. The lifetime prevalence of definite OCD was significantly higher in case than control first‐degree relatives (22.5% vs. 2.6%,P < 0.05). Compared to controls, case first‐degree relatives also had significantly higher lifetime rates of obsessions and compulsions (bothP < 0.05). There was no significant difference between case and control second‐degree relatives in lifetime rates of OCD. First‐degree relatives of case probands with ordering compulsions had a significantly higher lifetime rate of definite and subthreshold OCD than relatives of case probands without ordering compulsions (45.4% vs. 18.8%,P < 0.05). The lifetime prevalence of definite OCD was significantly higher in case first‐degree relatives with a history of tics than in case first‐degree relatives without a tic history (57.1% vs. 20.9%,P < 0.01). The results provide further evidence that early‐onset OCD is highly familial and suggest that two clinical variables are associated with its familial aggregation. © 2004 Wiley‐Liss, Inc.
Familial aggregation of schizophrenia‐spectrum disorders and obsessive‐compulsive associated disorders in schizophrenia probands with and without OCD
Authors: Poyurovsky Michael , Kriss Victoria , Weisman Gregory , Faragian Sarit , Schneidman Michael , Fuchs Camil , Weizman Abraham , Weizman Ronit
Published: January 2005

A substantial proportion of schizophrenia patients also has obsessive‐compulsive disorder (OCD). To further validate the clinical validity of a schizo‐obsessive diagnostic entity, we assessed morbid risks for schizophrenia‐spectrum disorders and OC‐associated disorders in first‐degree relatives of schizophrenia probands with and without OCD. Two groups of schizophrenia probands [with OCD (n = 57) and without OCD (n = 60)] and community‐based controls (n = 50) were recruited. One hundred eighty two first‐degree relatives of probands with OCD‐schizophrenia, 210 relatives of non‐OCD schizophrenia probands, and 165 relatives of community subjects were interviewed directly [59.3% (108/182), 51.9% (109/210), and 54.5% (90/165), respectively], using the Structured Clinical Interview for Axis‐I DSM‐IV Disorders and Axis II DSM‐III‐R Personality Disorders and the remaining relatives were interviewed indirectly, using the Family History Research Diagnostic Criteria. Relatives of OCD‐schiozphrenia probands had significantly higher morbid risks for OCD‐schizophrenia (2.2% vs. 0%; P = 0.033) and OCPD (7.14% vs. 1.90%; P = 0.014), and a trend towards higher morbid risk for OCD (4.41% vs. 1.43%; P = 0.08) compared to relatives of non‐OCD schizophrenia probands. When morbid risks for OCD, OCPD, and OCD‐schizophrenia were pooled together, the significant between‐group difference became robust (13.74% vs. 3.33%; P = 0.0002). In contrast, relatives of the two schizophrenia groups did not differ significantly in morbid risks for schizophrenia‐spectrum disorders, mood disorders, or substance abuse disorders. A differential aggregation of OC‐associated disorders in relatives of OCD‐schizophrenia versus non‐OCD schizophrenia probands, provides further support for the validity of a putative OCD‐schizophrenia (“schizo‐obsessive”) diagnostic entity. © 2004 Wiley‐Liss, Inc.
Organotins: Toxicology and biological effects
Authors: Nicklin S. , Robson M W
Published: January 2005

Organotins are currently one of the most studied groups of organometallic compounds; their novel and often unique chemical properties have intrigued chemists for over 100 years and, today, many of these compounds find extensive use in agriculture and industry. Over the years, however, a number of the organotins have been demonstrated to be toxic and there is now increasing concern that their widespread use may cause adverse effects within environmental and biological systems. This article reviews and updates the current literature concerning organotin toxicology. It identifies the various target organs and systems, discusses mechanisms and species susceptibility, and directs the reader to additional sources of more specialized information as appropriate.
Comparative studies of methylmercury determination in biological and environmental samples
Authors: Horvat M , May K , Stoeppler M , Byrne A R
Published: January 2005

Some parameters affecting the accuracy of various approaches to methylmercury (MeHg) determination in biological and environmental samples were studied. Different isolation techniques (ion‐exchange, extraction, volatilization, distillation) and final measurement via cold vapour atomic absorption spectroscopy (CV AA) or gas chromatography (GC) were compared. Results obtained by the various isolation techniques are comparable for almost all biological and environmental samples, except for soils and some sediments, where disagreement between the results obtained by GC and CV AA was found. In order to resolve these problems, a new separation technique based on distillation of MeHg from the sample followed either by CV AA or GC was developed. The new method results in very good recovery and reproducibility (95 ± 2%) for all samples examined (fish, mussel, shrimp, blood, hair, algae, sediment, etc.), is specific for MeHg and provides for its differentiation from other species by an indirect CV AA determination.

Gas‐chromatographic measurement of the isolated MeHg using different packings and conditioning of the columns is also discussed. The distillation method with GC detection is advantageous in producing cleaner chromatograms and in prolonging the life‐time of the packing and the intervals between reconditioning.
An improved method for the polymerization of ethynylferrocene. Conducting properties of doped polyethynylferrocene
Authors: Camus A , Faruffini V , Furlani A , Marsich N , Ortaggi G , Paolesse R , Russo M V
Published: January 2005

The catalytic activity of the [Rh(cod)Cl]2 complex (cod  cis, cis‐cyclo‐octa‐1,5‐diene) with respect to the polymerization of ethynylferrocene (EFc) was examined. A good yield (about 80%) of polyethynylferrocene (PEFc) was obtained in benzene by addition of sodium hydroxide as co‐catalyst. PEFc was insoluble in most organic solvents. The conductivity (s̀) of the undoped polymer is about 10−11 ohm−1 cm−1; upon doping PEFc with iodine in tetrahydrofuran the conductivity can be increased to 10‐100 ohm−1 cm−1. The influence of other doping agents was also examined.
Distribution of inorganic arsenic and methylated arsenic in marine organisms
Authors: Kaise Toshikazu , Hanaoka Ken'Ichi , Tagawa Shoji , Hirayama Teruhisa , Fukui Shozo
Published: January 2005

Inorganic arsenic and methylated arsenic compounds in 60 specimens of marine organisms were investigated by hydride generation derivatization and cold‐trap gas chromatography–mass spectrometry (GC MS). Chloroform–methanol extracts from seaweeds, shellfish, fish, crustaceans and other marine organisms were separated into water‐soluble and lipid‐soluble fractions. The arsenic compounds in each fraction were identified and analysed as arsine, methylarsine, dimethylarsine and trimethylarsine.

Trimethylarsenic compounds were distributed mainly in the water‐soluble fraction of muscle of carnivorous gastropods, crustaceans and fish. The amounts of dimethylated arsenic compounds were found to be larger than that of trimethylated arsenic in the lipid‐soluble fraction of fish viscera. Dimethylated arsenic compounds were distributed in the water‐soluble fraction of Phaeophyceae.
Simultaneous butyltin determinations in the microlayer, water column and sediment of a northern Chesapeake Bay marina and receiving system
Authors: Matthias Cheryl L , Bushong Steven J , Hall Lenwood W , Bellama Jon M , Brinckman F E
Published: January 2005

Butyltins were determined in the microlayer, water column and sediment of a northern Chesapeake Bay marina and its receiving system. Concentrations of the toxicant species tributyltin (TBT) ranged from 60 to 4130 ng dm−3in the microlayer, from 34 to 367 ng dm−3in the water column and from <0.05 to 1.4 m̈g g−1(dry weight) in sediment. TBT concentrations in all three environmental compartments were higher in the marinas than in the receiving system. Concentrations of TBT in the microlayer and water column of the study area were potentially toxic to sensitive aquatic biota. The microlayer appears to be depleted in dibutyltin relative to tributyltin compared to both water column and sediment.
Heterocycles derived from dichlorothiophene
Authors: Ai‐Soudani A‐R , Massey A G
Published: January 2005

A number of new, air‐stable heterocycles have been synthesized which contain 2,5‐dichlorothiophene groups as the structure‐forming units with sulphur, selenium, tellurium, phosphorus, arsenic, antimony, bismuth, tin and mercury acting as the hetero‐atoms.
An organoantimony catalyst for peptide synthesis; preparation and aminolysis of triphenylantimony bis(aminoacylate)s
Authors: Nomura R , Yamada Y , Matsuda H
Published: January 2005

Triphenylantimony bis(aminoacylate)s [Ph3Sb(OA)2, A = ZGly, ZPhe, ZLeu, BzPhe] were prepared by direct condensation between triphenylstibine oxide and N‐protected amino‐acids in acetone. The aminolysis of these antimony aminoacylates by amino‐acid esters gave corresponding dipeptides, which lead to a catalytic dipeptide synthesis using triphenylstibine oxide as a catalytic precursor of the antimony aminoacylate in situ.
The influence of clay minerals, oxides, and humic matter on the methylation and demethylation of mercury by micro‐organisms in freshwater sediments
Authors: Jackson Togwell A
Published: January 2005

Laboratory experiments and analysis of field samples showed that clay minerals, Fe and Mn oxides, and humic matter (colloids) have complex and often dramatic effects on the microbial methylation and demethylation of Hg, and on other microbial activities, in lake sediments. Depending on the nature, abundance, and surface chemistry of the colloids, the source of the sediment, the nature of the microbes, and synergistic/antagonistic effects of environmental variables, the colloids either strongly inhibited or stimulated the Hg transformations, had little or no effect, or alternated in their effects. Most of the results suggest specific effects on particular kinds of microbes, and are not attributable to general inhibition or stimulation of microbial growth or to effects due to the binding of Hg by the colloids. The colloids probably alter the species composition of the microbial community and affect the course of ecological succession, upsetting the dynamic balance between methylation and demethylation and causing alternate increases and decreases in methyl mercury (CH3Hg+) levels along with changes in other indicators of microbial activity [CO2 and CH4 production and oxidationreduction potential (Eh)].

The role of clays was critically dependent on surface coatings. Clays often interfered with methylation (while in some cases strongly promoting subsequent demethylation); but iron oxide (FeOOH) often promoted methylation, and FeOOH coatings on clay tended to counterbalance the negative influence of the clay. Removal of oxide coatings depressed both methylation and demethylation. Manganese oxide (MnOOH) coatings sometimes promoted methylation, but larger amounts of MnOOH (unlike FeOOH) strongly suppressed methylation. On addition of organic nutrients, oxide coatings enhanced methylation and impeded demethylation; without nutrient enrichment, the reverse tended to occur. Humic matter in solution tended to stimulate methylation; but humic coatings on clay impeded methylation and fostered demethylation. Thus, the effects of natural colloids on Hg speciation are vitally important but variable, inconsistent, and not altogether predictable.
The analyses of alkyllead compounds in fish and environmental samples in Ontario, Canada (1981–1987)
Authors: Wong P T S , Chau Y K , Yaromich J , Hodson P , Whittle M
Published: January 2005

Analyses of fish and other environmental samples (clams, macrophytes, sediments and waters) from areas upstream and downstream from two alkyllead manufactures beside the St Lawrence and St Clair Rivers, Ontario, show a clear indication of elevated alkyllead levels in samples near the industries. Most species of fish contained alkyllead compounds with tetraethyllead and triethyllead as the predominant forms. Most fish from the contaminated areas contained 50–75% of total lead as alkylleads. Carp, yellow perch and white sucker were generally the most contaminated species while pike, alewife and rock bass were the least contaminated. Average alkyllead levels varied from year to year but declined steadily after 1981. For example, the geometric mean of alkyllead compounds in carp from the St Lawrence River decreased from 4207 μg kg−1 in 1981 to 2000 μg kg−1 in 1982 and to 49 μg kg−1 in 1987, reflecting the reduction of alkylleads in the effluents and the closure of one of the manufactures in 1985. Alkyllead levels were consistently lower in muscle and carcass samples in comparison with whole fish containing fatty intestines. However, muscle levels were generally equal to carcass levels.

The concentrations of alkyllead compounds were generally low in clams, macrophytes, sediments and waters except from the immediate vicinity of the manufactures' final effluent discharges.
Studies of the naturally occurring biomethylation of selenium and the determination of the products
Authors: Jiang S G , Robberecht H , Adams F
Published: January 2005

A systematic study of the biomethylation of selenium and the determination of the methylated species indicates preliminarily that selenium is susceptible to natural biomethylation under certain environmental conditions. Detectable levels of methylated selenium species, including dimethyl selenide [(CH3)2Se], dimethyl diselenide [(CH3)2Se2] and dimethylselenone [(CH3)2SeO2] have been detected by gas chromatography – graphite furnace atomic absorption spectrophotometry (GC – GF AA) from a variety of environmental samples. Findings of naturally methylated selenium species from both soil samples and related air samples suggest that there may exist a localized cycle of selenium between ground soil and the ambient air.

Factors that influence the sensitivity and accuracy for the determination of alkyl selenide compounds by GC – GF AA have also been investigated. Flashlike injection mode and addition of about 10% of hydrogen gas to the argon carrier gas provide for highly sensitive detection. Reproducible determination can be obtained with a precision of about 6% and the detection limits are 0.3 ng Se m−3.
Optimization of butyltin measurements for seawater, tissue, and marine sediment samples
Authors: Stallard Martha O , Cola Susan Y , Dooley Carol A
Published: January 2005

Optimized techniques for measuring butyltins at the sub‐part‐per‐trillion (ppb; 1:1012) level in seawater and at the part‐per‐billion (ppb; 1:109) level in tissues and sediments are presented. Purge and trap/hydride derivatization followed by atomic absorption (AA) detection was optimized to give better sensitivity than was previously attained for seawater, yielding environmental detection limits of 0.08–0.2 ng dm−3. Improvement in precision and reproducibility in measurement of butyltins in tissues and sediments was attained by adjustment of the concentration in an organic extract to minimize matrix effects and by use of internal standards. The tissues and sediments were homogenized and extracted with methylene chloride (CH2Cl2) after acidification. The butyltins in the organic layer were derivatized with hexylmagnesium bromide and analyzed by gas chromatography (GC) with a flame photometric detector (FPD). The absolute detection limits in tissues and sedimets were 0.1 ng for tributyltin (TBT), 0.12 ng for dibutyltin (DBT) and 0.29 ng for monobutyltin (MBT).
Entwurfsoptimierung von Verbau und Wasserhaltung tiefer, wasserdichter Baugruben in bindigen Böden
Authors: Moormann Christian
Published: January 2005

Aktuelle Ausführungsbeispiele tiefer Baugruben in bindigen Böden zeigen, daß bei heute häufig als Regellösung Anwendung findenden, wasserdichten Baugrubenumschließungen die Erd‐ und Wasserdrucklasten mit zunehmender Baugrubentiefe so stark anwachsen, daß im Hinblick auf die aufzunehmenden Stützkräfte, die statisch erforderliche Einbindetiefe und die Biegemomentenbeanspruchung der Verbauwände sehr aufwendige Konstruktionen erforderlich werden und daß dabei – insbesondere bei tiefen, rückverankerten Baugruben – oft die Grenze der Ausführbarkeit erreicht wird. In diesen Fällen ist eine wasserdichte Verbauwandausführung nur möglich, wenn es gelingt, die großen Einwirkungen aus Wasserdruck und Strömungskräften zu reduzieren. In dem Beitrag werden Ansätze für eine Optimierung von Grundwasserhaltung und Verbaugestaltung tiefer, wasserdichter Baugruben in bindigen, durchlässigkeitsanisotropen Böden durch eine Reduktion der Wasserdruckbeanspruchung des Verbaus vorgestellt. Es werden Lösungsansätze zur Reduktion der Wasserlast durch eine Teil auflösung des Verbaus unterhalb der Baugrubensohle sowie durch Entspannungslanzen untersucht, vereinfachte Bemessungsansätze abgeleitet und Hinweise zur Entwurfsoptimierung formuliert.
Untersuchung zur Erddruckbeanspruchung von Winkelstützwänden
Authors: Achmus Martin , Rouili Ahmed
Published: January 2005

Die Bemessung des vertikalen Schenkels von Winkelstützwänden ist gemäß derzeitiger deutscher Normung für erhöhten Erddruck, d. h. den Mittelwert aus aktivem Erddruck und Erdruhedruck, vorzunehmen. Dieser Ansatz liegt, wie im vorliegenden Aufsatz gezeigt wird, in vielen Fällen deutlich auf der sicheren Seite. Mittels einer numerischen Parameterstudie werden die wesentlichen Einflußfaktoren aufgezeigt. Auf der Grundlage der Ergebnisse wird ein Verfahren vorgeschlagen, das die genauere Festlegung der Erddrucklast unter Berücksichtigung der wesentlichen Einflußgrößen in einfacher Weise ermöglicht.
Decision‐making competence: External validation through an individual‐differences approach
Authors: Parker Andrew M. , Fischhoff Baruch
Published: January 2005

This study asks to what extent (a) individuals show consistent performance differences across typical behavioral decision‐making tasks, and (b) how those differences correlate with plausible real‐world correlates of good decision making. Seven tasks, chosen to span the domain of decision‐making skills, were administered to participants in an ongoing longitudinal study providing extensive social, psychological, and behavioral measures. Performance scores on individual tasks generally showed small, positive inter‐task correlations. An aggregate measure of decision‐making competence (DMC) was appropriately correlated with plausible sources, concomitants, and outcomes of good decision making, suggesting the underlying construct's external validity. Higher DMC scores were associated with more intact social environments, more constructive cognitive styles, and fewer ‘maladaptive’ risk behaviors. In each case, DMC adds to the predictive validity of general measures of cognitive ability. These results suggest that poor decision making on common laboratory tasks is related to real‐world antecedents and consequences of poor decision making. Copyright © 2005 John Wiley & Sons, Ltd.
Structural and dynamic consequences of increasing repeats in a MUC1 peptide tumor antigen
Authors: Schuman Jason T. , Grinstead Jeffrey S. , Apostolopoulos Vasso , Campbell A. Patricia
Published: January 2005

MUC1 mucin is a large transmembrane glycoprotein whose extracelluler domain is composed of repeating units of a 20 amino acid sequence. In the cancer associated state, this protein expression becomes upregulated and underglycosylated. Previous studies, which show an enhanced binding of a 5‐repeat over a 1‐repeat MUC1 peptide to a panel of anti‐MUC1 antibodies, have led us to investigate the structural and dynamic consequences of increasing repeat number. Two MUC1 peptides were studied: a 16mer corresponding to slightly less than one full repeat of the MUC1 tandem repeat sequence (GVTSAPDTRPAPGSTA) and a 40mer corresponding to two full repeats of the MUC1 sequence (VTSAPDTRPAPGSTAPPAHG)2. Isotopically labeled versions of these MUC1 peptides were cloned, expressed, purified, and evaluated structurally and dynamically using 15N‐ and 13C‐edited NMR approaches. The data show that MUC1 structure, dynamics, and antibody binding affinity are invariant with increasing repeat number. In light of these results, we conclude that the enhanced antibody affinity of the 5‐repeat over the 1‐repeat MUC1 peptide is due to multivalency effects, and not due to the development of higher order structure in the longer length peptides. The implications of these results are discussed within the context of a multiple repeat MUC1 breast cancer vaccine design. © 2005 Wiley Periodicals, Inc. Biopolymers, 2005
Fast-track surgery
Authors: Kehlet H , Wilmore D W
Published: January 2005

Not yet fully implemented
Systematic review of hyperbaric oxygen in the management of chronic wounds
Authors: Roeckl-Wiedmann I , Bennett M , Kranke P
Published: January 2005

Background

Many therapeutic options exist for chronic wounds. Hyperbaric oxygen therapy (HBOT) is one such option. It may be used for diabetic, venous, arterial and pressure ulcers.

Methods

Following a systematic search of the literature, pooled analyses of predetermined clinical outcomes of randomized controlled trials involving the use of HBOT for chronic wounds were performed. Relative risks (RR) and number needed to treat (NNT) with 95 per cent confidence intervals (c.i.) were calculated.

Results

Six studies met the inclusion criteria. No appropriate trials were located for arterial and pressure ulcers. Pooled data from five trials on diabetic ulcers (118 patients) suggested a significant reduction in the risk of major amputation with HBOT (RR: 0·31; c.i. 0·13 to 0·71) with a NNT of 4 (c.i. 3 to 11). Sensitivity analyses did not alter the results. Ulcer healing and the rate of minor amputation were not influenced by HBOT. Data from one trial on venous ulcers suggested significant wound size reduction at the end of the treatment, but not at follow-up.

Conclusions

There is evidence that HBOT reduces the risk of major amputation in diabetic patients. For venous, arterial or pressure ulcers there is a lack of data. Further trials may be warranted.
Radical Cations of Phenyl‐Substituted Aziridines: What Are the Conditions for Ring Opening?
Authors: Gaebert Carsten , Mattay Jochen , Toubartz Marion , Steenken Steen , Müller Beat , Bally Thomas
Published: January 2005

Radical cations were generated from different phenyl‐substituted aziridines by pulse radiolysis in aqueous solution containing TlOH.+, N3.or SO4.−as oxidants or inn‐butyl chloride, by60Co γ radiolysis in Freon matrices at 77 K, and in some cases by flash photolysis in aqueous solution. Depending on the substitution pattern of the aziridines, two different types of radical cations are formed: if the N atom carries a phenyl ring, the aziridine appears to retain its structure after oxidation and the resulting radical cation shows an intense band at 440–480 nm, similar to that of the radical cation of dimethylaniline. Conversely, if the N atom carries an alkyl substituent while a phenyl ring is attached to a C‐atom of the aziridine, oxidation results in spontaneous ring opening to yield azomethine ylide radical cations which have broad absorptions in the 500–800 nm range. In aqueous solution the two types of radical cations are quenched by O2with different rates, whereas inn‐butyl chloride, the ring‐closed aziridine radical cations are not quenchable by O2. The results of quantum chemical calculations confirm the assignment of these species and allow to rationalize the different effects that phenyl rings have if they are attached in different positions of aziridines. In the pulse radiolysis experiments in aqueous solution, the primary oxidants can also be observed, whereas inn‐butyl chloride a transient at 325 nm remains unidentified. In the laser flash experiments, both types of radical cations were also observed.
Deep‐seated, well differentiated lipomatous tumors of the chest wall and extremities
Authors: Bassett Mikelle D. , Schuetze Scott M. , Disteche Christine , Norwood Thomas H. , Swisshelm Karen , Chen Xiaoqin , Bruckner James , Conrad Ernest U. , Rubin Brian P.
Published: January 2005

BACKGROUND

Intramuscular lipomas and atypical lipomatous tumors (ALT) are common deep‐seated lipomatous tumors of the chest wall and extremities. Distinguishing between these two entities can be difficult based on histologic analysis alone. However, the cytogenetic profiles of ALT and intramuscular lipomas are distinct. Correct classification is important, because aggressive local disease recurrence occurs more frequently in patients with ALT than in patients with intramuscular lipoma. The authors examined their single institutional experience and correlated their classification with clinical features and outcome.

METHODS

In the current study, 106 patients with deep‐seated, well differentiated adipose tumors of the chest wall and extremities were classified as having ALT or intramuscular lipoma using a combined approach of histology and cytogenetics, if available. The classification was correlated with clinicopathologic features and follow‐up data.

RESULTS

Fifty‐five patients were classified as having intramuscular lipoma and 51 were classified as having ALT. Classification did not correlate with age and gender (P = 0.28 and P = 0.96, respectively). Intramuscular lipomas were smaller than ALTs (P < 0.0001), but there was significant overlap between the 2 groups. ALT occurred preferentially in the lower extremity (P < 0.0009). Four percent of patients with intramuscular lipomas and 27% of patients with ALTs developed local disease recurrence (P = 0.0006). Disease recurrence did not correlate with patient age at diagnosis, patient gender, tumor size, and tumor location (P = 0.45, P = 0.26, P = 0.49, and P = 0.28, respectively). Within the subset of patients with ALTs, disease recurrence did not correlate with patient age at diagnosis, patient gender, or tumor location (P = 0.38, P = 0.54, and P = 0.86, respectively).

CONCLUSIONS

Classification of deep‐seated, well differentiated lipomatous tumors of the extremities and chest wall using a combined approach of histology and cytogenetics correlated well with biologic behavior/disease recurrence. This combined approach is advocated to better stratify patients for treatment purposes and follow‐up. Cancer 2005. © 2004 American Cancer Society.
A pseudopotential SCF‐MO study of Te
Authors: Rothman Michael J. , Bartell Lawrence S. , Ewig Carl S. , Van Wazer John R.
Published: January 2005

A recently developed ab initio pseudopotential molecular orbital approach was applied to the Te ion, a system outside the practical reach of conventional all‐electron treatments. Computations were carried out with a minimal STO‐4G basis set. Results account reasonably well for the observed optical absorption spectrum and suggest the origin of a hitherto unassigned weak band. Ground‐state properties, which included the structure, force field, and vibrational frequencies, were also investigated. Treated as a free, gas‐phase ion, tetratellurium (II) yielded a bond length 0.05 Å shorter than the experimental value for the ion in a crystal lattice. Placement of static, point‐charge counterions in the Te coordination sphere increased the bond length to a value 0.005 Å longer than derived by experiment. Calculations on neutral, cyclic Te4 provided a theoretical single‐bond reference length 0.09 Å longer than that obtained for the ion in a counterion environment. Comparisons between observed and calculated frequencies suggest an assignment of the vibrational spectrum different from the provisional assignment in the literature.
Integrated spatial electron populations in molecules: Application to simple molecules
Authors: Collins John B. , Streitwieser Andrew
Published: January 2005

The electron projection function P(x, z) = ∫ ρ(x, y, z) dy is used to evaluate charge transfer and covalency in two series of molecules, LiX and CH3X (X = Li, BeH, BH2, CH3, NH2, OH, and F), with wavefunctions derived from STO‐3G, 4‐31G, and, in some cases, 6‐31* ab initio calculations. The precision of the method and comparison with Mulliken populations analysis are described. Particular attention is given to CH3Li which by our criteria is wholly ionic.
Microcomputer‐aided instruction and research in group theory
Authors: Trindle Carl
Published: January 2005

A collection of programs which aid in the use of group theory has been developed for the Apple II. The programs automate much of the tedious algebra necessary to generate character tables and representation matrices from the properties of the operators chosen to generate the group. At the same time, the presentation of intermediate results provides a schematic guide to the procedures by which groups are constructed. The choice of generators is not limited to the reflections, rotations, and inversions, which are the familiar features of chemical group theory. Any generator representable as a permutation may be treated; thus general permutation groups and Longuet‐Higgins groups may be studied. As an illustration we describe the states of beryllium borohydride, which require a form of Longuet‐Higgins group theory.
Treatment of multiexponential decay data by the method of zero determinants
Authors: Szamosi Janos , Schelly Z. A.
Published: January 2005

The principles of a new method, the method of zero determinants, are described which can be used for the determination of the number of exponentials in accurate, multiexponential decay curves, as well as for the smoothing of multiexponential experimental data. It is based on the idea that the determinant of an overdetermined data matrix for accurate data is zero. The method is not limited by mathematical approximations, and thus uncovers the decay curve hidden in the data set.
A theoretical study on the protonation of cycloalkanes CnH2n (n = 3 to 6)
Authors: Lee Choi Chuck , Hass Ernst C. , Obafemi Craig A. , Mezey Paul G.
Published: January 2005

Ab initio self‐consistent‐field molecular orbital calculations have been carried out for the CnH2n (n = 3 to 6) cycloalkanes and various conformers of their protonated forms. The calculated protonation energies for the sequence of conformers of the protonated forms follow the experimentally observed trend. Correlations between optimum CCC bond angles at the protonation site and the calculated protonation energies have been observed, and these correlations may be of some use in estimating protonation energy‐bond angle relations in other (strained) cyclic compounds when the central carbon atom of a CCC moiety is protonated.
Reliable Gaussian basis sets for closed‐shell atoms
Authors: Radzio Elżbieta , Andzelm Jan
Published: January 2005

Medium size Gaussian basis sets for inert‐gas atoms (from neon to xenon) have been constructed using the energy optimization method which maintains reliable description of the long‐range valence atomic region. These basis sets have been tested in SCF calculations on homonuclear inert‐gas dimers. For Ne2, Ar2, and Kr2, the present results have been analyzed carefully and compared with those obtained using extended basis sets (for Kr2 extended benchmark calculations are also reported). Our interation energies agree well with accurate values and are compared with experimental data. For Ne2 and Ar2, detailed studies of basis set superposition error also are presented.
Quantum mechanical modeling of a transannular interaction in a bicyclic amidinium ion
Authors: Edwards W. Daniel , Weisman Gary R.
Published: January 2005

A transannular donor‐acceptor interaction in a bicyclic azaamidinium salt was modeled by quantum mechanical calculations using a supermolecule complex consisting of a formamidinium cation and an ammonia molecule. Molecular properties are reported at various geometries. These results are compared with the results of similar calculations on the bicyclic cation itself. The model calculations and the bicyclic cation calculations are in good agreement, but both fail to reproduce the experimentally known structure. Results from ab initio calculations on the model system are discussed, as are results from calculations which included iodide as counterion.
Molecular mechanics and the deformation of macromolecules: The use of a very short cutoff combined with a quadratic approximation
Authors: Karfunkel H. R.
Published: January 2005

An approximation to the molecular mechanical treatment of structural deformations of macromolecules is presented. The method is based on a partitioning of the conformational energy into three parts. The first part is covered by the condensed potential functions which absorb many short‐range nonbonding interactions. The second part consists of a few nonbonded interactions below a very short cutoff radius of 4 Å. The third part, consisting of the vast majority of pairwise interactions, is approximated by a quadratic expression confined to a subspace of the conformational space. A detailed computational example on LH‐RH, including an analysis of the errors resulting from other conventional approximation methods, is given. A comparison to the conventional cutoff approximation used in x‐ray refinement delivers a speedup factor of at least two orders of magnitude.
The MMP2 calculational method
Authors: Sprague Joseph T. , Tai Julia C. , Yuh Young , Allinger Norman L.
Published: January 2005

The molecular mechanics (MMP2) program and procedures for the treatment of conjugated hydrocarbons, and some of the results which they can achieve are described. The program is an updated version of the similar MMP1 program, but contains some differences. It is based on an SCF π system calculation, rather than on the VESCF method used earlier. All parameters are compatible with those in the MM2 program. Hence it is possible to calculate heats of formation, resonance energies, and structures for conjugated hydrocarbons in a way that is consistent with the calculations on non‐conjugated molecules. The overall results as far as structure and energy are somewhat better than they were with the MMP1 program.
Configurational specificity of stacking interactions in DNA base pairs: A computational analysis
Authors: Sanyal Nitish K. , Roychoudhury M. , Ruhela Kavita R. , Tiwari Sugriva Nath
Published: January 2005

A theoretical study of stacking patterns of various hydrogen‐bonded base pair complexes has been undertaken. Modified Rayleigh‐Schrodinger perturbation theory for intermediate range interactions, has been employed to evaluate the stacking interactions using multicentered‐multipole expansion method. Net atomic charge and corresponding dipole components located at each of the atomic centers have been computed by CNDO/2 method. An analysis of the intermolecular forces involved in the stable formation of the various base pair complexes, has been presented and the results have been discussed in the light of experimental as well as other theoretical observations. The possibility of relative preference of the left‐handed configuration for alternating sequences has been quantitatively explored.
Algorithm for rapid calculation of Hessian of conformational energy function of proteins by supercomputer
Authors: Wako Hiroshi , Gō Nobuhiro
Published: January 2005

An improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long‐range, nonbonded interactions are cut off and long‐range electrostatic interactions are approximated by dipole‐dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different sizes.
Strategies for vectorizing the sparse matrix vector product on the CRAY XMP, CRAY 2, and CYBER 205
Authors: Bauschlicher Charles W. , Partridge Harry
Published: January 2005

Large randomly sparse matrix vector products are important in a number of applications in computational chemistry, such as matrix diagonalization and the solution of simultaneous equations. Vectorization of this process is considered for the CRAY XMP, CRAY 2, and CYBER 205, using a matrix of dimension of 20 000 with from 1% to 6% nonzeros. Efficient SCATTER/GATHER capabilities add coding flexibility and yield significant improvements in performance. For the CYBER 205, it is shown that minor changes in the IO can reduce the CPU time by a factor of 50. Similar changes in the CRAY codes make a far smaller improvement.
A specific inhibitor design approach by means of molecular dynamics calculation for porcine pancreatic elastase
Authors: Fujita T.
Published: January 2005

A 27‐picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme‐ligand complex between porcine pancreatic elastase (PPE) and acetyl‐alanine‐proline‐alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root‐mean‐square fluctuations (RMSF) increased compared with the x‐ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65‐Å high‐resolution x‐ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen‐bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic data previously reported.
Strain energy minimization study of the mechanism of, and the barrier to, conformational interconversion in five‐membered diamine chelate rings
Authors: Hambley Trevor W.
Published: January 2005

The method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two‐dimensional analysis of the conformational interconversion from δ‐ to λ‐[Co(ethane‐1,2‐diamine) (NH3)4]3+ reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7 kJ mol−1. Substitution at the carbon atoms, variation of the metal‐nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol−1 for (N,N,N′,N′‐tetramethylethane‐1,2‐diamine) [(NH3)4]3+.
Molecular valence calculations on cyclohexasulfur, cycloheptasulfur, and cyclooctasulfur
Authors: Laitinen Risto S. , Randolph Bruce , Pakkanen Tapani A.
Published: January 2005

A theoretical study of homocyclic sulfur species S6, S7, and S8 was carried out using a molecular valence method involving stepwise approximations for orthogonality and core‐valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all‐electron ab initio results. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing time.
Basis sets for molecular interactions. 1. Construction and tests on (HF)2 and (H2O)2
Authors: Latajka Zdzislaw , Scheiner Steve
Published: January 2005

Basis set superposition error (BSSE) remains one of the major difficulties besetting current ab initio calculations of molecular interactions. Despite the widespread notion that lowering of the BSSE to negligible magnitude requires extremely large basis sets, we show that simple modifications of basis sets of only moderate size (e.g., 6‐31G**) can accomplish the same end at much reduced computational expense. These modifications include reoptimization of the orbital exponents within the framework of the relevant molecules, plus addition of a single diffuse shell of sp orbitals on nonhydrogen centers. Subsequent addition of a second set of d‐functions further lowers the SCF BSSE, bringing it below 0.1 kcal/mol for both (HF)2 and (H2O)2. It is notable that addition of the latter d‐functions without prior reoptimization of the valence orbitals produces the opposite effect of an increase in the BSSE. Although the MP2 BSSE is also substantially decreased by the above modifications, it appears difficult to reduce this quantity below about 0.4 kcal/mol.
The stepwise heats of hydrogenation of barrelene, an ab initio study
Authors: Schmitz Lawrence R. , Allinger Norman L. , Flurchick Kenneth M.
Published: January 2005

Ab initio Hartree‐Fock calculations at the 6–31G*//3–21G level of theory are reported for bicyclo[2.2.2]‐2,5,7‐octatriene (barrelene), 1, bicyclo[2.2.2]‐2,5‐octadiene, 2, bicyclo[2.2.2]‐2‐octene, 3, and bicyclo‐[2.2.2]octane, 4. The stepwise heats of hydrogenation of 1 were found to be 38.1, 31.8, and 28.4 kcal/mol, respectively. The unusually large heat of hydrogenation for the first double bond is attributed to the destabilizing electronic effects involving the interaction of the three double bonds of 1.
One‐center expansion for pseudopotential matrix elements
Authors: Pelissier M. , Komiha N. , Daudey J. P.
Published: January 2005

Semilocal pseudopotential operators can be expressed as a linear combination of nonlocal (projection) operators. Pseudopotential operator integrals over a molecular basis set are therefore reduced to linear combinations of overlap integrals products. Molecular calculations indicate that sufficient precision can be achieved with a limited number of nonlocal operators. Analytic derivatives of pseudopotential integrals are easily deduced and implemented in a standard quantum chemistry program.
Quantum mechanics of pseudorotation in ring systems: An application of the MuMATH symbolic algebra system
Authors: Trindle Carl
Published: January 2005

A variety of quantum mechanical models have guided the interpretation of the far infrared (IR) spectrum of easily deformed ring systems, but an explicit guide to such modelling would ease further analysis. The coordinates introduced by Cremer and Pople provide a starting point for description of puckering, separate from other internal motions of a ring system. For a ring of N atoms there are N‐3 puckering modes, composed of [N ‐ (2)/2] pseudorotation “amplitudes” and [(N ‐ 3)/2] “angles.” (The brackets [] mean “truncate to the integer.”) Separation of the Schroedinger equation is possible for the “free puckerer,” the “puckerer in a box,” and for puckering opposed by a separable harmonic potential; in this latter case the energy is determined and the state is labeled by a set of pseudorotation quantum numbers Mk and radial quantum numbers nk:

Here vk is the harmonic frequency for the k‐th mode, and h is Planck's constant. Since most ring systems are nonharmonic, and require a distinct “quartic‐puckering” potential for each puckering mode, a perturbation treatment of the quartic terms is required. We provide formulas and a symbolic algebra computer program to generate expressions for integrals needed for the perturbation or linear variation modeling.
The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space
Authors: Lipton Mark , Still W. Clark
Published: January 2005

A general algorithm is described which exhaustively searches conformational space using an internal coordinate tree search. Using only geometrical operations and a set of criteria for eliminating chemically unreasonable structures, the algorithm generates starting geometries for optimization by molecular mechanics. An implementation of this algorithm is exceedingly fast and finds all known minima, as well as several new ones, for four test alkanes. This method makes feasible global conformational searches for molecules with up to 109 conformational possibilities.
Construction of the best set of four orthonormal 2s‐2p hybrid orbitals by least‐squares methods
Authors: Laube Thomas
Published: January 2005

A least‐squares procedure for the construction of four 2s‐2p hybrid orbital direction vectors that deviate least from four given bond vectors emanating from a tetravalent atom is described. The procedure is used as a tool for the interpretation of structural data from X‐ray diffraction, electron diffraction, and microwave experiments.