bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robert Rosen in the Age of Systems Biology
Authors: Thomas S. Randall 
Published: October 2007

AbstractThe widespread use of the term Systems Biology (SB) signals a welcome recognition that organisms must be understood as integrated systems. Although just what this is taken to mean varies from one group to another, it generally implies a focus on biological functions and processes rather than on biological parts and a reliance on mathematical modeling to arrive at an understanding of these biological processes based on biological observations or measurements. SB, thus, falls directly in the line of reflection carried out by Robert Rosen throughout his work. In the present article, we briefly introduce the various currents of SB and then point out several ways Rosen's work can be used to avoid certain pitfalls associated with the use of dynamical systems models for the study of complex systems, as well as to inspire a productive path forward based on loosely organized cooperation among dispersed laboratories.
Exploring the Temporal Consequences of Chasing the Elements in Rosen's Relational Diagrams
Authors: Prideaux Jeffrey A. 
Published: October 2007

AbstractIn the work ‘Life Itself’, Rosen showed that a formal mechanism cannot be ‘closed to efficient cause’. Additionally, he claimed that organisms are ‘closed to efficient cause’ and that, by logical extension, organisms cannot be mechanisms. This paper shows that it is possible for mechanisms to be ‘nearly closed to efficient cause’, with the requirement that some unentailed efficient‐cause agents are placed inside the system. Populations of these ‘nearly closed to efficient cause’ systems can be defined based on the ability to isolate each component in its own ‘reaction chamber’. Diagrams from these populations are drawn from a couple of different perspectives, and comments are made on how these diagrams can be related to the more conventional language of chemistry.
Variation, Natural Selection, and Information Content – A Simulation
Authors: Testa Bernard , Bojarski Andrzej J. 
Published: October 2007

AbstractIn Neo‐Darwinism, variation and natural selection are the two evolutionary mechanisms that propel biological evolution. Variation implies changes in the gene pool of a population, enlarging the genetic variability from which natural selection can choose. But in the absence of natural selection, variation causes dissipation and randomization. Natural selection, in contrast, constrains this variability by decreasing the survival and fertility of the less‐adapted organisms.The objective of this study is to propose a highly simplified simulation of variation and natural selection, and to relate the observed evolutionary changes in a population to its information content. The model involves an imaginary population of individuals. A quantifiable character allows the individuals to be categorized into bins. The distribution of bins (a histogram) was assumed to be Gaussian. The content of each bin was calculated after one to twelve cycles, each cycle spanning N generations (N being undefined). In a first study, selection was simulated in the absence of variation. This was modeled by assuming a differential fertility factor F that increased linearly from the lower bins (F<1.00) to the higher bins (F>1.00). The fertility factor was applied as a multiplication factor during each cycle. Several ranges of fertility were investigated. The resulting histograms became skewed to the right. In a second study, variation was simulated in the absence of selection. This was modeled by assuming that during each cycle each bin lost a fixed percentage of its content (variation factor Y) to its two adjacent bins. The resulting histograms became broader and flatter, while retaining their bilateral symmetry. Different values of Y were monitored. In a third study, various values of F and Y were combined.Our model allows the straightforward application of Shannon's equation and the calculation of a Shannon‐entropy (SE) values for each histogram. Natural selection was, thus, shown to result in a progressive decrease in SE as a function of F. In other words, natural selection, when acting alone, progressively increased the information content of the population. In contrast, variation resulted in a progressive increase in SE as a function of Y. In other words, variation acting alone progressively decreased the information content of a population. When both factors, F and Y, were applied simultaneously, their relative weight determined the progressive change in SE.
Water as a Complex System: Its Role in Ligand Diffusion, General Anesthesia, and Sleep
Authors: Kier Lemont B. 
Published: October 2007

AbstractThe work and inspiration of Robert Rosen is stated and expressed in personal tones. The concept of passages through water (H2O) near protein surfaces is reviewed in terms of it's influence on ligand diffusion to an effector. This is offered as a target for interference by a non‐specific general anesthetic agent. In view of the similarities between this anesthetic state and sleep, this mechanism is proposed to be operative for the sleep/wake states. Based on this mechanism and other factors, nitrogen (N2) is proposed as an exogenous sleep factor.
Causality and Complexity: The Myth of Objectivity in Science
Authors: Mikulecky Donald C. 
Published: October 2007

AbstractTwo distinctly different worldviews dominate today's thinking in science and in the world of ideas outside of science. Using the approach advocated by Robert M. Hutchins, it is possible to see a pattern of interaction between ideas in science and in other spheres such as philosophy, religion, and politics. Instead of compartmentalizing these intellectual activities, it is worthwhile to look for common threads of mutual influence. Robert Rosen has created an approach to scientific epistemology that might seem radical to some. However, it has characteristics that resemble ideas in other fields, in particular in the writings of George Lakoff, Leo Strauss, and George Soros. Historically, the atmosphere at the University of Chicago during Hutchins' presidency gave rise to Rashevsky's relational biology, which Rosen carried forward. Strauss was writing his political philosophy there at the same time. One idea is paramount in all this, and it is Lakoff who gives us the most insight into how the worldviews differ using this idea. The central difference has to do with causality, the fundamental concept that we use to build a worldview. Causal entailment has two distinct forms in Lakoff 's analysis: direct causality and complex causality. Rosen's writings on complexity create a picture of complex causality that is extremely useful in its detail, grounding in the ideas of Aristotle. Strauss asks for a return to the ancients to put philosophy back on track. Lakoff sees the weaknesses in Western philosophy in a similar way, and Rosen provides tools for dealing with the problem.This introduction to the relationships between the thinking of these authors is meant to stimulate further discourse on the role of complex causal entailment in all areas of thought, and how it brings them together in a holistic worldview. The worldview built on complex causality is clearly distinct from that built around simple, direct causality. One important difference is that the impoverished causal entailment that accompanies the machine metaphor in science is unable to give us a clear way to distinguish living organisms from machines. Complex causality finds a dichotomy between organisms, which are closed to efficient cause, and machines, which require entailment from outside. An argument can be made that confusing living organisms with machines, as is done in the worldview using direct cause, makes religion a necessity to supply the missing causal entailment.
A Promising Method for Phosphinidene Generation: Complexes of Phosphinidenes with N‐Donor ligands
Authors: Benkõ Zoltán , Gudat Dietrich , Nyulászi László 
Published: October 2007

Abstract1,3,2‐diazaphospholenes and related compounds can formally be regarded as complexes of phosphinidenes (RP) with 1,4‐diazabutadienes. The dissociation Gibbs free energies of these “complexes” were calculated by using density functional theory (B3LYP/3‐21G(*) and B3LYP/6‐311+G**). The dissociation Gibbs free energies show systematic dependence on the phosphorus substituent as well as on the stability of the N‐donor ligand formed as a byproduct. The thermodynamics and kinetics of the dissociations were thoroughly examined. The results allow us to conclude that novel routes of phosphinidene generation can be developed.
Total Synthesis and Selective Activity of a New Class of Conformationally Restrained Epothilones
Authors: Alhamadsheh Mamoun M. , Gupta Shuchi , Hudson Richard A. , Perera Lalith , Tillekeratne L. M. Viranga 
Published: October 2007

AbstractStereoselective total syntheses of two novel conformationally restrained epothilone analogues are described. Evans asymmetric alkylation, Brown allylation, and a diastereoselective aldol reaction served as the key steps in the stereoselective synthesis of one of the two key fragments of the convergent synthetic approach. Enzyme resolution was employed to obtain the second fragment as a single enantiomer. The molecules were assembled by esterification, followed by ring‐closing metathesis. In preliminary cytotoxicity studies, one of the analogues showed strong and selective growth inhibitory activity against two leukemia cell lines over solid human tumor cell lines. The precise biological mechanism of action and high degree of selectivity of this analogue remain to be examined.
The determination of the absolute configurations of chiral molecules using vibrational circular dichroism (VCD) spectroscopy
Authors: Stephens Philip J. , Devlin Frank J. , Pan Jian‐Jung 
Published: October 2007

AbstractThe vibrational circular dichroism (VCD) spectra of the two enantiomers of a chiral molecule are of equal magnitude and opposite sign: i.e. mirror‐image enantiomers give mirror‐image VCD spectra. In principle, the absolute configuration (AC) of a chiral molecule can therefore be determined from its VCD spectrum. In practice, the determination of the AC of a chiral molecule from its experimental VCD spectrum requires a methodology which reliably predicts the VCD spectra of its enantiomers. The only reliable methodology developed to date uses the Stephens quantum‐mechanical theory of the rotational strengths of fundamental vibrational transitions, developed in the early 1980s, implemented using ab initio density functional theory in the GAUSSIAN program in the mid 1990s. This methodology has by now been widely used in determining ACs from experimental VCD spectra. In this article we discuss the protocol for determining the ACs of chiral molecules with optimum reliability and its implementation for a variety of molecules, including the D3 symmetry perhydrotriphenylene, a thiazino‐oxadiazolone recently shown to be a highly active calcium entry channel blocker, the alkaloid natural products schizozygine, iso‐schizogaline, and iso‐schizogamine, and the iridoid natural products plumericin, iso‐plumericin, and prismatomerin. The power of VCD spectroscopy in determining ACs, even for large organic molecules and for substantially conformationally‐flexible organic molecules is clearly documented. Chirality, 2008. © 2007 Wiley‐Liss, Inc.
Vom Zucker zum Ethanol: Eine experimentgestützte Erarbeitung von Stoffwechselvorgängen bei der Gärung
Authors: Heimann Rebekka , Müller Karina 
Published: October 2007

AbstractBei der alkoholischen Gärung, zu der z.B. die Hefe befähigt ist, werden Zucker wie Rohrzucker (Saccharose), Traubenzucker (Glucose) und Fruchtzucker (Fructose) zu Ethanol und Kohlenstoffdioxid abgebaut. Dies läuft über komplexe biochemische Prozesse. Die in diesem Beitrag dargestellte Konzeption soll Schülerinnen und Schülern einen aktiven Zugang zur Thematik der Gärung bei Hefe ermöglichen, indem Teilschritte der Gärung experimentell untersucht werden und historisch relevante Überlegungen zum Verlauf der Gärung einbezogen und überprüft werden. Es werden zumeist einfach realisierbare Experimente zur Spaltung des Rohrzuckers in Traubenzucker und Fruchtzucker vorgestellt. Ein weiteres Experiment beschäftigt sich mit der Spaltung des Zwischenprodukts Brenztraubensäure zu Acetaldehyd und Kohlenstoffdioxid. Außerdem wird gezeigt, dass Hefe die Fähigkeit besitzt, Stoffe zu reduzieren, eine Fähigkeit, die sie z.B. für die Reduktion von Acetaldehyd zum Endprodukt Ethanol benötigt.Bei der Bearbeitung der Frage nach dem Verlauf der Gärung wird deutlich, dass einzelne Experimente nicht zum Ziel führen, sondern Aussagen erst durch Kombination verschiedener Befunde möglich werden. Dadurch kann das kritische Auswerten experimenteller Beobachtungen geschult werden.Das Reaktionsschema der Gärung wird in vereinfachter Form behandelt und kann durch die Formulierung des Reaktionsverlaufs mit Summen‐ und Konstitutionsformeln ergänzt werden. Weitere Informationen zur didaktischen Reduktion der Glycolyse, also des Abbaus vom Zucker bis zur Brenztraubensäure, findet man in [11], Informationen zum Glucoseabbau im menschlichen Körper z.B. in [12].
Kombinatorische Chemie oder: Wie kann man den Aufwand bei der Suche nach neuen Wirkstoffen verringern?
Authors: Pustowka Patricia , Bader Hans Joachim 
Published: October 2007

AbstractEin wesentliches Ziel naturwissenschaftlichen Unterrichts ist es, Basiskonzepte der zugrunde liegenden Wissenschaften sowie deren Verknüpfung mit der Lebens‐ und Alltagswelt der Schülerinnen und Schüler zu vermitteln. Bedenkt man die wenigen naturwissenschaftlichen Konzepte und die geringen chemischen Kenntnisse, die viele Erwachsene aus der Schulzeit in ihr Berufs‐ und Alltagsleben „hinüberretten”︁, so muss dieses Ziel äußerst ernst genommen werden. Vor diesem Hintergrund ist die Forderung nach einer Beschränkung des Stoffes und einer Konzentration auf Wesentliches zu stellen.Allerdings befindet sich die Chemiedidaktik hier in einem Dilemma: Das Grundwissen ist klar definierbar, der Bezug zur Lebens‐ und Alltagswelt ändert sich aber laufend. Neue Kraftstoffe auf pflanzlicher Basis oder Lithium‐Polymer‐Zellen für Laptops und Handys sind nur zwei Beispiele. Werden ausschließlich petrostämmige Kraftstoffe und der Bleiakkumulator behandelt, verzichtet der Unterricht auf wichtige Bezüge und vermittelt ein mehr und mehr historisches Bild der Chemie.Ohne Zweifel kann und soll jedoch im Chemieunterricht nicht jede Neuentwicklung berücksichtigt werden. Das gilt ganz besonders dann, wenn nicht übergreifende Prinzipien, sondern Kenntnisse über Einzelverbindungen, Details von Reaktionen oder Verfahren zur Diskussion stehen. Grundsätzliche und weit tragende neue Ansätze dürfen aber nicht negiert werden. Diese Gefahr besteht besonders dann, wenn neue Strategien, Entwicklungen oder Ergebnisse nicht unmittelbar im Alltag sichtbar, gleichwohl aber von hoher Bedeutung in Forschung und Entwicklung sind.Wir konzentrieren uns in unseren derzeitigen Arbeiten dar auf, solche grundlegenden neuen wissenschaftlichen Strategien exemplarisch für den Chemieunterricht zugänglich zu machen. Im vorliegenden Beitrag werden schulchemische Ansätze vorgestellt, die zeigen, wie durch die Anwendung so genannter kombinatorischer Methoden die Suche nach Substanzen mit bestimmten Eigenschaftsprofilen gestaltet werden kann.
Die Reaktion von Ethanol mit Magnesium und Zink
Authors: Schelle Thomas , Strecker Hans , Habekost Achim 
Published: October 2007

AbstractUm Sauerstoff in organischen Verbindungen nachzuweisen, wird in den meisten Schulbüchern der Versuch Ethanol reagiert mit Magnesium herangezogen, bei dem das Magnesium durch den im Ethanol chemisch gebundenen Sauerstoff oxidiert werden soll. Nach Auskunft der Schulbücher soll dabei ausschließlich Wasserstoff entstehen, wie etwa die Abb. 1 aus einem Schulbuch [1] nahe legt: Man erhält weder in der Abbildung noch im Text einen Hinweis auf weitere gasförmige Produkte außer auf Wasserstoff. Unklar ist zudem, was mit den Ethanolrest passiert, dem der Sauerstoff entzogen wurde und ob tatsächlich Magnesiumoxid entsteht.
Heparanase up‐regulation in tongue cancer
Authors: Nagler Rafael , Ben‐Izhak Ofer , Cohen‐Kaplan Victoria , Shafat Itay , Vlodavsky Israel , Akrish Sharon , Ilan Neta 
Published: October 2007

AbstractBACKGROUND.Heparanase up‐regulation has been correlated with reduced postoperative survival in various cancers.METHODS.Heparanase expression was analyzed in 60 consenting tongue (mobile) cancer patients by means of immunohistochemistry. Heparanase levels were also analyzed in the saliva of both healthy controls and tongue cancer patients using a novel heparanase enzyme‐linked immunosorbent assay method.RESULTS.Heparanase staining was positive (>0) in 92% and negative (=0) in 8% of the tumors and staining intensity correlated with tumor size and tumor stage. Moreover, the survival probability of patients negative for heparanase (=0) at 60 months was 100%, compared with only 41% for patients positive for heparanase (>0), suggesting that heparanase may serve as a prognostic factor for this malignancy and an attractive target for anticancer drug development. Heparanase was detected in the saliva of healthy controls and the mean concentration was determined as 119 ± 37 pg/mL. Importantly, a nearly 3‐fold increase of heparanase levels was detected in saliva collected from tongue cancer patients (334 ± 69 pg/mL), a difference that is statistically highly significant (P = .004).CONCLUSIONS.These findings support heparanase up‐regulation in tongue cancer and raise the possibility of using this simple test as a diagnostic tool to monitor tongue cancer progression and response to treatment. Cancer 2007. © 2007 American Cancer Society.
Molecule‐Enhanced Surface‐Enhanced Infrared Absorption Spectroscopy (MOSEIRA)
Authors: Kosower Edward M. , Markovich Gil , Borz Galina 
Published: October 2007

AbstractSurface‐enhanced infrared absorption spectroscopy (SEIRA) of methanol, ethanol, 1‐propanol, and 2‐propanol in thin films on planar silver halide (AgX) fibers under slow N2 flow using 1 sec scans reveals structure in absorbance–time plots. The absorption intensities show extra enhancements (3×) in the absorbance (OH stretch) ascribed to oligomers present at the AgX surface (molecule enhanced, thus MOSEIRA).This is above those due to amplification (40×, 20 reflections) and enhancement (30×, image dipoles or surface phonon polaritons). In the case of ethanol an excellent initial pentamer spectrum evolves over 8–10 min to a mixture of pentamer, tetramer, and trimer spectra that within another minute forms small oligomers and monomers. We use a new type of cell for infrared spectroscopy containing an AgX planar fiber. The optical configuration leads to a vicinal region at the surface defined by evanescent waves. Within this region are surface‐induced organized species such as ethanol oligomers. The planar AgX fiber supports 20 reflections and transmits light over a wide visible–infrared wavelength range. Short scan times permit the study of volatile substrates or solvents, including the effects of solvent polarity.
Characteristics and key findings for ‘Vaccines for women to prevent neonatal tetanus’
Authors: van Dalen Elvira , Offringa Martin , Kremer Leontien 
Published: October 2007

AbstractThese are the characteristics and key findings for a Cochrane review, published in this issue of EBCH, first published as: Demicheli V, Barale A, Rivetti A. Vaccines for women to prevent neonatal tetanus. Cochrane Database of Systematic Reviews 2005, Issue 4. Art. No.: CD002959. DOI: 10.1002/14651858.CD002959.pub2.Further information for this Cochrane review is available in this issue of EBCH in the accompanying EBCH Summary and Commentary articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration
Characteristics and key findings for ‘Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease’
Authors: van Dalen Elvira , Offringa Martin , Kremer Leontien 
Published: October 2007

AbstractThese are the characteristics and key findings for a Cochrane review, published in this issue of EBCH, first published as: Hirst C, Owusu‐Ofori S. Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease. Cochrane Database of Systematic Reviews 2002, Issue 3. Art. No.: CD003427. DOI: 10.1002/14651858.CD003427.Further information for this Cochrane review is available in this issue of EBCH in the accompanying EBCH Summary and Commentary articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration
Characteristics and key findings for ‘Therapeutic interventions for Burkitt’s lymphoma in children'
Authors: van Dalen Elvira , Offringa Martin , Kremer Leontien 
Published: October 2007

AbstractThese are the characteristics and key findings for a Cochrane review, published in this issue of EBCH, first published as: Okebe JU, Lasserson TJ, Meremikwu MM, Richards S. Therapeutic interventions for Burkitt's lymphoma in children. Cochrane Database of Systematic Reviews 2006, Issue 4. Art. No.: CD005198. DOI: 10.1002/14651858.CD005198.pub2.Further information for this Cochrane review is available in this issue of EBCH in the accompanying EBCH Summary and Commentary articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration
Summary of ‘Corticosteroids for treating dengue shock syndrome’
Authors: Milne Andrea 
Published: October 2007

AbstractThis is a summary of a Cochrane review, published in this issue of EBCH, first published as: Panpanich R, Sornchai P, Kanjanaratanakorn K. Corticosteroids for treating dengue shock syndrome. Cochrane Database of Systematic Reviews 2006, Issue 3. Art. No.: CD003488. DOI: 10.1002/14651858.CD003488.pub2.Further information for this Cochrane review is available in this issue of EBCH in the accompanying Commentary and Characteristics and Key Findings Tables articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration
Summary of ‘Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease’
Authors: Milne Andrea 
Published: October 2007

AbstractThis is a summary of a Cochrane review, published in this issue of EBCH, first published as: Hirst C, Owusu‐Ofori S. Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease. Cochrane Database of Systematic Reviews 2002, Issue 3. Art. No.: CD003427. DOI: 10.1002/14651858.CD003427.Further information for this Cochrane review is available in this issue of EBCH in the accompanying Commentary and Characteristics and Key Findings Tables articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration
Commentary on ‘Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease’
Authors: Raphael Jean L. , Mueller Brigitta U. 
Published: October 2007

AbstractThis is a commentary on a Cochrane review, published in this issue of EBCH, first published as: Hirst C, Owusu‐Ofori S. Prophylactic antibiotics for preventing pneumococcal infection in children with sickle cell disease. Cochrane Database of Systematic Reviews 2002, Issue 3. Art. No.: CD003427. DOI: 10.1002/14651858.CD003427.Further information for this Cochrane review is available in this issue of EBCH in the accompanying EBCH Summary and Characteristics and Key Findings Tables articles. Copyright © 2007 The Cochrane Collaboration. Published by John Wiley & Sons, Ltd. The Cochrane Collaboration