bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Barrier to Internal Rotation in Ethane
Authors: Lowe J. P. 
Published: October 2006

The internal rotation barrier in ethane appears susceptible to "explanation" at a qualitative, intuitively useful, reasonably correct level. At this level, localized and delocalized MO's each produce a description.
For a rigid rotation, the delocalized description is basically the "orbital control" type familiar from Woodward-Hoffmann rules, Walsh's rules, and the formation of diatomic molecules. This description indicates that long-range eclipsed H---H antibonding is responsible for the barrier. The equivalent localized-bond description invokes destructive interference or repulsion between eclipsed C-H bonds. The extension of this kind of description to other molecules requires care.
Subsequent to rigid rotation, the relaxation of ethane into its optimum eclipsed geometry produces almost no energy change but produces an unknown degree of energy "redistribution."
I have emphasized that the theoretical distinction between "orbital control" and "steric interaction" is not precise and that a clarification in terminology may be desirable in this connection.
The discussion of barriers given here applies only to a limited class of molecules, exemplified by ethane. No doubt, additional factors enter into a proper description of barriers in molecules having lower symmetry or more polar bonds, or both.
Finally, I should point out that approaches other than those in categories 1 to 3 have been made in efforts to rationalize or predict barriers to internal rotation. The Hellmann-Feynman theorem has been applied to find the torque on ethane at conformations between staggered and eclipsed . The integral Hellmann-Feynman theorem has served as a basis for discussing barriers in terms of transition densities and has led to an electrostatic model for barriers which has given some remarkably successful barrier predictions. These approaches are mathematically valid, and it is perfectly legitimate to try to extract physical explanations from them also. Thus, several valid explanations for the barrier to internal rotation in ethane are possible. However, I feel that the explanations proposed above in terms of delocalized or localized orbitals are preferable at present inasmuch as they are couched in terms and concepts currently in the mainstream of chemical thinking.
Assembly of Bacterial Ribosomes
Authors: Nomura Masayasu 
Published: October 2006

I have not mentioned the remarkable progress made mainly by Fellner and his co-workers in the elucidation of the primary structure of rRNA's and by Wittmann and his co-workers in determining the structure of several ribosomal proteins. Such knowledge of primary structures is certainly the basis of complete understanding of the structure of the ribosome. With the current progress in technology, complete elucidation of the primary structure of all the ribosomal components is probably a matter of time. As indicated in this article, a rough approximation of the three-dimensional structure of ribosomes is likely to emerge soon. Although not mentioned in this article, studies of ribosomes from higher organisms are also progressing. We must, therefore, consider what further studies should be conducted and what kinds of questions we would like to solve.
Some groups of investigators aim to elucidate the complete three-dimensional structure of ribosomes and to find out how these complex cell organelles function; they hope to determine the conformational changes of many of the component molecules within the ribosome structure in response to external macromolecules and cofactors engaged in protein synthesis. Such knowledge will also be important in enabling us to understand the regulation of translation of genetic messages. Other groups of investigators aim to elucidate the complex series of events which originate in the transcription of the more than 60 genes and culminate in the formation of the specific structure of the organelle. Complete reproduction in vitro of all the assembly events that occur in vivo should not be difficult to achieve in principle. It should then become possible to study in vitro any factor regulating the biogenesis of the organelle. Although we do not know whether such studies would reveal any new fundamental principle that governs the complex circuits of interconnected macromolecular interactions, the achievement of such a complete in vitro system would represent a necessary step in the comprehensive understanding of biogenesis of organelles, and eventually, of the more complex behavior and genesis of cells.
Department of Defense R & D in the University
Authors: Glantz Stanton A. , Albers Norm V. 
Published: October 2006

The DOD carefully evaluates its technical needs and executes programs of sponsored research and development to fulfill them. Thus, while individual projects proceed in accordance with established scientific principles of objectivity, the overall system of DOD funding allows the military to influence the development of science technology. Many have argued that this system of contracts and grants has well served science and the universities. One cannot deny that the influx of money led to rapid progress in selected scientific fields and increased scientific institutions' affluence. With this fact we have no quarrel. However, these same people often continue to argue that the systems of federal funding for science, specifically DOD funding of science, follows merely on the work's scientific merit, not on how it fits any larger scheme. They continue, that, since DOD supports good science for its own sake, the combination of military money and universities strongly encouraging faculty to seek that money encourages healthy competition for faster scientific progress. The DOD's approval process is seen to follow from the scientist up, with the military deciding which proposals for research have the most intrinsic (scientific) merit, then after the fact, thinking up a military justification for congressional budget requests. It is this latter belief with which we take issue. The DOD considers the scientific worth of the proposals for research it receives, but only after it has determined that the proposal fulfills a specific military need.
This fact and its implications for the university as an institution charged with protecting the process by which man discovers new knowledge have been ignored in the debates over DOD sponsored research and development in universities. In addition, the Nixon Administration's efforts to tighten management controls over civilian research, especially in the biomedical and energy areas, promises to further undermine the university's role as an institution charged with fostering a search for truth free from bias in both methodology and subject selection.
Permethylpolysilanes: Silicon Analogs of Hydrocarbons
Authors: West Robert , Carberry Edward 
Published: October 2006

Studies of the spectra of cyclopolysilanes have led to several significant conclusions. These molecules possess both easily ionized Si-Si bonding electrons and low energy delocalized antibonding orbitals, and can therefore serve either as electron donors or acceptors. This model explains the similarity in properties between cyclopolysilanes and aromatic hydrocarbons. Further investigations of cyclopolysilanes seem likely to provide the key to understanding of controversial questions of bonding in metalloid compounds even as studies of their carbon analogs, the cyclic and cage hydrocarbons, have been crucial to present knowledge of organic stereochemistry and reaction mechanisms.
The reactions of cyclopolysilanes are not only interesting in themselves, but have opened the way to the synthesis of complex polysilanes and thus to whole new areas of study. Improved methods of synthesis and isolation are needed, but the number and kinds of compounds that can be prepared seem almost limitless. Perhaps a polymetal chemistry comparable in breadth and variety to carbon chemistry is now developing.
Development of a PCR Assay Followed by Nonradioactive Hybridization Using Oligonucleotides Covalently Bound to CovaLink NH Microwells for Detection of Four
Plasmodium
Species in Blood Samples from Humans
Authors: Machouart M. , Bigois-Delemotte L. , Ajana F. , Brizion M. , Biava M. F. , Collomb J. , Fortier B. 
Published: September 2006

ABSTRACT

We developed and evaluated a PCR-based assay to detect four
Plasmodium
species in 79 blood samples from 56 travelers returning from areas where malaria is endemic. DNA amplification targeting a small region of the 18S rRNA gene was performed with
Plasmodium
genus-specific primers. The biotinylated PCR products were then identified by PCR-colorimetric Covalink NH microwell plate hybridization (CMPH) using species-specific phosphorylated probes covalently bound to a pretreated polystyrene surface. The results from PCR-CMPH showed high specificity, and for 47 of the 56 patients (84%), microscopy and PCR-CMPH results were in agreement. Discordant results were reevaluated with microscopy examination, other molecular methods, and DNA sequencing. Except for one patient, discrepancies were resolved in favor of PCR-CMPH: three mixed infections were detected, four species identification errors were corrected, and two negative results were shown to be positive. Our results indicate that PCR-CMPH is a simple, rapid, and specific method for malaria diagnosis. It employs stable reagents and inexpensive equipment, making it suitable for routine epidemiological use.
Real-Time PCR Assay for Detection and Quantification of Hepatitis B Virus Genotypes A to G
Authors: Welzel Tania M. , Miley Wendell J. , Parks Thomas L. , Goedert James J. , Whitby Denise , Ortiz-Conde Betty A. 
Published: September 2006

ABSTRACT

The detection and quantification of hepatitis B virus (HBV) DNA play an important role in diagnosing and monitoring HBV infection as well as assessing therapeutic response. The great variability among HBV genotypes and the enormous range of clinical HBV DNA levels present challenges for PCR-based amplification techniques. In this study, we describe the development, evaluation, and validation of a novel real-time PCR assay designed to provide accurate quantification of DNA from all eight HBV genotypes in patient plasma specimens. A computer algorithm was used to design degenerate real-time PCR primers and probes based upon a large number (
n
= 340) of full-length genomic sequences including HBV genotypes A to H from Europe, Africa, Asia, and North and South America. Genotype performance was tested and confirmed using 59 genotype A to G specimens from two commercially available worldwide genotype panels. This assay has a dynamic range of at least 8 log
10
without the need for specimen dilution, good clinical intra- and interassay precision, and excellent correlation with the Bayer Diagnostics VERSANT HBV DNA 3.0 (branched DNA) assay (
r
= 0.93). Probit analysis determined the 95% detection level was 56 IU/ml, corresponding to 11 copies per PCR well. The high sensitivity, wide linear range, good reproducibility, and genotype inclusivity, combined with a small sample volume requirement and low cost, make this novel quantitative HBV real-time PCR assay particularly well suited for application to large clinical and epidemiological studies.
Molecular Phylogeny of
Sporothrix schenckii
Authors: Marimon Rita , Gené Josepa , Cano Josep , Trilles Luciana , Dos Santos Lazéra Márcia , Guarro Josep 
Published: September 2006

ABSTRACT

The pathogenic dimorphic fungus
Sporothrix schenckii
is the agent responsible for sporotrichosis, an important fungal infection with a worldwide distribution. Little is known about the population structure of
S. schenckii
, although recent molecular and phenotypic data seem to demonstrate that different genetic lineages exist within this species. The aim of this study was to determine, by sequence analysis of three protein coding loci (chitin synthase, β-tubulin, and calmodulin), whether this variability is due to species divergence or intraspecific diversity in
S. schenckii
. We included in the analysis 60 isolates (59 of clinical and 1 of environmental origin) of this species from a wide geographical range. DNA sequence data from the three nuclear regions were used in a phylogenetic analysis. The combined analysis of the three loci revealed the presence of three major clades, one grouping all of the European isolates, another with only Brazilian isolates, and the third with isolates from other South American countries and Africa. A total of 14 100% bootstrap-supported nodes were shown, 6 of them representing putative phylogenetic species. Our data also demonstrated that most of these species prevail in different geographical regions.
Evaluation of the New Chromogenic Medium Candida ID 2 for Isolation and Identification of
Candida albicans
and Other Medically Important
Candida
Species
Authors: Eraso Elena , Moragues María D. , Villar-Vidal María , Sahand Ismail H. , González-Gómez Nagore , Pontón José , Quindós Guillermo 
Published: September 2006

ABSTRACT

The usefulness of Candida ID 2 (CAID2) reformulated medium (bioMérieux, France) has been compared with that of the former Candida ID (CAID; bioMérieux), Albicans ID 2 (ALB2; bioMérieux), and CHROMagar Candida (CAC; Chromagar, France) chromogenic media for the isolation and presumptive identification of clinically relevant yeasts. Three hundred forty-five stock strains from culture collections, and 103 fresh isolates from different clinical specimens were evaluated. CAID2 permitted differentiation based on colony color between
Candida albicans
(cobalt blue; sensitivity, 91.7%; specificity, 97.2%) and
Candida dubliniensis
(turquoise blue; sensitivity, 97.9%; specificity, 96.6%).
Candida tropicalis
gave distinguishable pink-bluish colonies in 97.4% of the strains in CAID2 (sensitivity, 97.4%; specificity, 100%); the same proportion was reached in CAC, where colonies were blue-gray (sensitivity, 97.4%; specificity, 98.7%). CAC and CAID2 showed 100% sensitivity values for the identification of
Candida krusei
. However, with CAID2, experience is required to differentiate the downy aspect of the white colonies of
C. krusei
from other white-colony-forming species. The new CAID2 medium is a good candidate to replace CAID and ALB2, and it compares well to CAC for culture and presumptive identification of clinically relevant
Candida
species. CAID2 showed better results than CAC in some aspects, such as quicker growth and color development of colonies from clinical specimens, detection of mixed cultures, and presumptive differentiation between
C. albicans
and
C. dubliniensis
.
Genital
Candida
Species Detected in Samples from Women in Melbourne, Australia, before and after Treatment with Antibiotics
Authors: Pirotta Marie V. , Garland Suzanne M. 
Published: September 2006

ABSTRACT

Vulvovaginal candidiasis (VVC) remains a common cause of morbidity, with three-quarters of women affected during their lifetimes. Use of antibiotics is an acknowledged trigger for VVC, which adversely affects women's physical and emotional health. Knowledge of patterns of genital
Candida
species-level identification is important for management, as
Candida
species other than
Candida albicans
often fail first-line treatment. A community sample of women with no vaginal symptoms, and who were prescribed antibiotics, was recruited into this study, where the incidence of genital colonization by various
Candida
species was documented, as well as symptoms of VVC plus relevant associations, before and after treatment with antibiotics. Self-collected low vaginal swabs were taken prior to and 8 days after completion of antibiotic treatment, and data on various potential risk factors for VVC were collected simultaneously, with complete data being available for 233 participants. Baseline
Candida
species colonization was present in 21% of women (95% confidence intervals [CI], 17% to 27%), rising to 37% (95% CI, 31% to 44%) after antibiotic treatment. The primary species detected for either period was
C. albicans
(73%), with
Candida glabrata
detected in around 20%. Self-assessed proneness to VVC after antibiotic treatment and baseline colonization with
Candida
spp. were significantly associated with symptomatic VVC after antibiotic treatment. For microbiologically proven candidiasis, VVC symptoms had a sensitivity of 57% and a specificity of 91%. When physicians prescribe antibiotics, the history of risk of VVC is one issue that physicians should discuss with women, particularly those who are self-identified as being prone to VVC. Furthermore, we recommend that definitive microbiological diagnoses be made for women with recurrent symptoms or those failing initial treatment, to guide appropriate therapy.
Two Cases of Infections Due to Multidrug-Resistant
Bacteroides fragilis
Group Strains
Authors: Katsandri Anastasia , Papaparaskevas Joseph , Pantazatou Angeliki , Petrikkos Georgios L. , Thomopoulos Georgios , Houhoula Dimitra P. , Avlamis Athina 
Published: September 2006

ABSTRACT

Bacteroides fragilis
group strains are still considered susceptible to most antimicrobial agents used for the treatment of infections caused by anaerobic organisms. We describe two cases of infections due to isolates simultaneously resistant to clindamycin, tetracycline, cefoxitin, piperacillin-tazobactam, and imipenem and, in one of the two cases, to metronidazole. Such infections, although still rare, do exist and tend to complicate treatment.
Comparative Evaluation of Early Diagnosis of Tuberculous Meningitis by Different Assays
Authors: Quan Chao , Lu Chuan-Zhen , Qiao Jian , Xiao Bao-Guo , Li X. 
Published: September 2006

ABSTRACT

Cerebrospinal fluid (CSF) and peripheral blood (PBL) were sampled multiple times from 25 patients with a clinical diagnosis of tuberculous meningitis (TBM) and 49 controls, including 27 patients with other infectious diseases of the central nervous system and 22 patients with other noninfectious neurological diseases. We used an enzyme-linked immunospot assay (ELISPOT) to detect anti-
Mycobacterium bovis
BCG antibody-secreting cells in CSF and PBL, PCR to detect a repeated insertion sequence (IS
6110
) specific for
Mycobacterium tuberculosis
in CSF, and an enzyme-linked immunosorbent assay (ELISA) to detect anti-BCG antibodies in CSF and PBL. In the meantime, culture of CSF from every TBM and control patient was done on Lowenstein-Jensen medium. ELISPOT proved to be the most valuable test, with a sensitivity of 84.0% and a specificity of 91.8%, and showed a sensitivity of 100.0% with the CSF specimens obtained within 4 weeks after the onset of TBM. The numbers of CSF anti-BCG immunoglobulin-secreting cells tested by ELISPOT were even higher in the early phase of TBM and declined while the disease was going on (
P
= 0.008), which allowed an early diagnosis to be made. The sensitivities of PCR and ELISA were only 75.0% and 52.3%, respectively; and the specificities were 93.7% and 91.6%, respectively. Culture of CSF on Lowenstein-Jensen medium was the least sensitive (16%) compared to the sensitivities of the other three assays. Our results demonstrate that the ELISPOT technique is worthy for routine use in the laboratory to support the clinical diagnosis of TBM.
Detection of Cariogenic
Streptococcus mutans
in Extirpated Heart Valve and Atheromatous Plaque Specimens
Authors: Nakano Kazuhiko , Inaba Hiroaki , Nomura Ryota , Nemoto Hirotoshi , Takeda Munehiro , Yoshioka Hideo , Matsue Hajime , Takahashi Toshiki , Taniguchi Kazuhiro , Amano Atsuo , Ooshima Takashi 
Published: September 2006

ABSTRACT

The involvement of oral bacteria in the pathogenesis of cardiovascular diseases has been the focus of attention in many studies, and several periodontal pathogens have been detected in diseased cardiovascular lesions, suggesting relationships between oral microorganisms and cardiovascular diseases. However, no information is available regarding the involvement of cariogenic pathogens such as
Streptococcus mutans
. The presence of oral streptococcal species and periodontitis-related bacteria in 35 heart valve and 27 atheromatous plaque clinical specimens, as well as 32 dental plaque specimens from the same subjects, was analyzed using a PCR method. Furthermore, broad-range PCR with DNA sequencing analysis was employed to identify the bacterial species in those samples.
Streptococcus mutans
was frequently detected in the heart valve (69%) and atheromatous plaque (74%) specimens, while other bacterial species, including those related to periodontitis, were detected with much lower frequencies. The bacterial composition in cardiovascular tissues was found to be markedly distinct from that in dental plaque, with only a limited number of species, including
S. mutans
, in the cardiovascular regions shown to have possibly originated from the oral cavity. Semiquantitative assay results revealed that
S. mutans
was detected in significant quantities in the heart valve (40%) and atheromatous plaque (48%) specimens, whereas the quantities of all other tested bacterial species, including several related to periodontitis, were negligible in the cardiovascular samples. These results indicate that
S. mutans
is a possible causative agent of cardiovascular disease.
Optimization and Validation of Recombinant Serological Tests for African Swine Fever Diagnosis Based on Detection of the p30 Protein Produced inTrichoplusia niLarvae
Authors: Pérez-Filgueira D. M. , González-Camacho F. , Gallardo C. , Resino-Talaván P. , Blanco E. , Gómez-Casado E. , Alonso C. , Escribano J. M. 
Published: September 2006

ABSTRACTWe describe the validation of an enzyme-linked immunosorbent assay (ELISA) and confirmatory immunoblotting assays based on a recombinant p30 protein (p30r) produced in insect larvae using a baculovirus vector. Such validation included the following: (i) the scaling up and standardization of p30r production and the associated immunoassays, (ii) a broad immunological analysis using a large number of samples (a total of 672) from Spain and different African locations, and (iii) the detection of the ASF virus (ASFV)-antibody responses at different times after experimental infection. Yields of p30r reached up to 15% of the total protein recovered from the infected larvae at 3 days postinfection. Serological analysis of samples collected in Spain revealed that the p30r-based ELISA presented similar sensitivity to and higher specificity than the conventional Office International des Epizooties-approved ASFV ELISA. Moreover, the p30r ELISA was more sensitive than the conventional ELISA test in detecting ASFV-specific antibodies in experimentally infected animals at early times postinfection. Both the recombinant and conventional ELISAs presented variable rates of sensitivity and specificity with African samples, apparently related to their geographical origin. Comparative analyses performed on the sequences, predicted structures, and antigenicities of p30 proteins from different Spanish and African isolates suggested that variability among isolates might correlate with changes in antigenicity, thus affecting detection by the p30r ELISA. Our estimations indicate that more than 40,000 ELISA determinations and 2,000 confirmatory immunoblotting tests can be performed with the p30r protein obtained from a single infected larva, making this a feasible and inexpensive strategy for production of serological tests with application in developing countries.