bluuebunny/crossref_metadata_2025_split huggingface dataset:
SBRML: a markup language for associating systems biology data with models
Authors: Dada Joseph O. , Spasić Irena , Paton Norman W. , Mendes Pedro 
Published: February 2010

Abstract
Motivation: Research in systems biology is carried out through a combination of experiments and models. Several data standards have been adopted for representing models (Systems Biology Markup Language) and various types of relevant experimental data (such as FuGE and those of the Proteomics Standards Initiative). However, until now, there has been no standard way to associate a model and its entities to the corresponding datasets, or vice versa. Such a standard would provide a means to represent computational simulation results as well as to frame experimental data in the context of a particular model. Target applications include model-driven data analysis, parameter estimation, and sharing and archiving model simulations.
Results: We propose the Systems Biology Results Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each dataset is represented as a series of values associated with model variables, and their corresponding parameter values. SBRML provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes. We present and discuss several examples of SBRML usage in applications such as enzyme kinetics, microarray gene expression and various types of simulation results.
Availability and Implementation: The XML Schema file for SBRML is available at http://www.comp-sys-bio.org/SBRML under the Academic Free License (AFL) v3.0.
Contact: pedro.mendes@manchester.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Anterior development in the parthenogenetic and viviparous form of the pea aphid, Acyrthosiphon pisum: hunchback and orthodenticle expression
Authors: Huang T.‐Y. , Cook C. E. , Davis G. K. , Shigenobu S. , Chen R. P.‐Y. , Chang C.‐C. 
Published: February 2010

AbstractIn the dipteran Drosophila, the genes bicoid and hunchback work synergistically to pattern the anterior blastoderm during embryogenesis. bicoid, however, appears to be an innovation of the higher Diptera. Hence, in some non‐dipteran insects, anterior specification instead relies on a synergistic interaction between maternally transcribed hunchback and orthodenticle. Here we describe how orthologues of hunchback and orthodenticle are expressed during oogenesis and embryogenesis in the parthenogenetic and viviparous form of the pea aphid, Acyrthosiphon pisum. A. pisum hunchback (Aphb) mRNA is localized to the anterior pole in developing oocytes and early embryos prior to blastoderm formation – a pattern strongly reminiscent of bicoid localization in Drosophila. A. pisum orthodenticle (Apotd), on the other hand, is not expressed prior to gastrulation, suggesting that it is the asymmetric localization of Aphb, rather than synergy between Aphb and Apotd, that regulates anterior specification in asexual pea aphids.
Changes in specific domains of sexual function and sexual bother after radical prostatectomy
Authors: Le Jesse D. , Cooperberg Matthew R. , Sadetsky Natalia , Hittelman Adam B. , Meng Maxwell V. , Cowan Janet E. , Latini David M. , Carroll Peter R. 
Published: February 2010

Study Type – Therapy (outcomes research) Level of Evidence 2cOBJECTIVETo quantitatively assess the effect of radical prostatectomy (RP) on the specific domains that comprise overall sexual function (SF), focusing on the relationships among these domains and overall SF, and to identify predictors for recovery of SF over time, as a decline in SF and sexual bother (SB) are known potential complications of treatment for prostate cancer.PATIENTS AND METHODSWithin the Cancer of the Prostate Strategic Urologic Research Endeavor database, we identified men diagnosed between 1995 and 2001 with localized prostate cancer treated with RP. SF and SB outcomes, measured using the University of California Los Angeles Prostate Cancer Index, were assessed at 6‐month intervals for 4 years after RP.RESULTSIn all, 620 men met the study criteria; at 6 months after RP, overall and all the specific domains of SF declined, with improvement in most specific domains by 2 years after RP. The greatest declines were in the ability to achieve erections, high‐quality erections, and frequent erections; these domains were also most strongly correlated with overall SF. Sexual desire was relatively preserved, and there was a weak correlation between overall SF and sexual desire after RP, when there was the greatest discrepancy between sexual desire and other domains of function. SB showed continued improvement over time to 4 years but was not well correlated with any measurements of SF assessed. Younger age, college education, sexual aid and medication use, the absence of comorbid conditions, and nerve‐sparing surgery were predictive of significant recovery of function in several specific domains of SF.CONCLUSIONSRP affects specific domains of SF to differing degrees. Compromised erectile function is most commonly reported among these specific domains and seems to play a more dominant role in determining overall SF, but notably none of the domains of function were closely linked to SB. Because education is protective in the perception of bother, appropriate counselling and the setting of expectations for outcomes in overall and specific domains of SF might lead to improved quality of life after treatment for prostate cancer.
SCIENCE AND SERIOUS THEOLOGY: TWO PATHS FOR SCIENCE AND RELIGION'S FUTURE?
Authors: Hallanger Nathan J. 
Published: February 2010

Abstract.Although they take different approaches, both Taede A. Smedes and Kevin Sharpe have challenged the theology‐and‐science enterprise and raised important questions about theological and scientific assumptions behind this work. Smedes argues that theology should be taken more seriously, and Sharpe believes that theology should be more scientific. A proposed middle way involves engaging in the dialogue itself and exploring the questions and methodological implications that arise in the context of problem‐focused interactions.
Das Concilium Quinisextum (691/692). Neue Erkenntnisse über ein umstrittenes Konzil und seine Teilnehmer
Authors: Flogaus Reinhard 
Published: February 2010

Abstract
One of the two oldest manuscripts of Greek canon law, the Codex Patmiacus 172, sheds new light on the history of the Council in Trullo (691/92). Whereas from the other 45 extant manuscripts only 220 episcopal signatures to this Council have been known so far, the Patmiacus has preserved 6 additional signatures and thus raises the number of the hitherto known clerical participants to 226, representing a total of 227 bishoprics. Since these subscriptions are preceded by the signature of the Emperor, the Patmiacus is the sole extant manuscript that bears in fact a total of 227 signatures, the number of participants assigned to this Council in the later canonistic tradition. Besides, this manuscript offers a great number of additions and corrections to the other 220 signatures. Due to the discovery of the six new episcopal signatures, however, the question of authenticity of the six position markers found in some manuscripts to indicate the place for the signatures of six episcopal sees which were present at the Sixth Ecumenical Council in 681/82 but apparently absent in 691/92 must be reconsidered. Whereas so far these markers have been considered original because it was only by their connumerating that the number of 227 could be achieved, this argument has become obsolete by the subscription list of the Patmiacus. Furthermore, the missing of the first three markers in the oldest extant manuscripts as well as their odd positions makes it very likely that they are not original but were interpolated at the times of the Seventh Ecumenical Council in order to assimilate the beginning of the subscription list of the Council of 691/92 to the one of 681/82 and thus substantiating Tarasios' claim that the Council in Trullo was a continuation of the Sixth Ecumenical Council. Whether the West and the metropolitan sees present in 681/82 - Rome, Thessaloniki, Sardinia, Ravenna and Corinth - were in fact invited as well to the Council in 691/92 is once again an open question and cannot be answered by reference to the manuscript tradition. Finally, the reasons for the western opposition to this Council are not so much to be sought in the form of the subscription list but more in the content of the canons and the Logos Prosphonetikos.
The anonymous progymnasmata in John Doxapatres' Homiliae in Aphthonium
Authors: Gibson Craig A. 
Published: February 2010

Abstract
This article examines the anonymous progymnasmata in John Doxapatres' commentary on Aphthonius' Progymnasmata for evidence about their authorship, origin, and relations to other progymnasmata. These exercises include three chreias, a refutation and confirmation of the myth of Ganymedes, an encomium and invective of Agamemnon, a comparison of the grapevine and olive tree, and an ethopoeia on the deposition of the emperor Michael V Kalaphates. In addition to providing a formal rhetorical analysis of the exercises, the article offers further support for the view of R. F. Hock and E. N. O'Neil (The Chreia and Ancient Rhetoric: Classroom Exercises, 2002) that Doxapatres did not compose these exercises and that they all derive from a single collection. In an appendix, it argues that George Pachymeres, in his comparison of the olive tree and grapevine, used the anonymous comparison in Doxapatres and not the four parallel exercises by Ps.-Nicolaus.
Über die Liebe der Byzantiner zum Rindfleisch
Authors: Koder Johannes 
Published: February 2010

Abstract
An article published several years ago on the provision of Constantinople with meat came to the conclusion (which had already been postulated a priori at the beginning of the paper) that beef had always played a considerable role in the Byzantine kitchen. A reexamination of the written sources (some considered by the author as well as many others) and some archaeological evidence (neglected by the author) allows for the following conclusions: The Byzantines used horned cattle (and buffalos) mainly as working and draught animals, in some regions also for dairy produce. Although the Byzantines did not avoid eating beef (nor was this forbidden by any religious precept), archaeological evidence generally indicates that beef was only occasionally consumed, and then only such animals as old dairy cows and plough oxen slaughtered before dying a natural death. In some instances, however, written sources mention foreigners, e. g. soldiers from other lands, as consumers of beef.
Damnata verba: censure di Pletone in alcuni codici platonici
Authors: Pagani Fabio 
Published: February 2010

Abstract
This paper explores the historical and palaeographical features linking together three manuscripts of Plato that bear - as previous researchers have shown - marginalia and textual corrections in the hand of the Byzantine humanist George Gemistos Pletho: Marc. Gr. 188 and 189 and Laur. 80, 19. There is, however, one more astonishing peculiarity associating precisely these three manuscripts: at several points there are erasures of passages dealing with ancient theology or with pagan myths and gods.
The first part of this study provides a general analysis of the censored passages, showing that they are part of a coherent project aiming at altering Plato's theology: in the manuscripts in his possession Pletho radically altered Plato's text, sometimes improving it, but sometimes censoring or entirely rewriting it; it is this very distinctive text of Plato that circulated in his school. In the second part, Pletho's acts of censorship as a whole are compared with his philosophical ideas as they can be reconstructed from the surviving portions of his Laws (Nomoi), proving that he tried to remove discrepancies between Plato and himself. In the third part of the essay, the ideological reasons for this censorship are investigated, with a special focus on the relations between Pletho's manuscripts and some miscellaneous codices belonging to his students or circulating in the platonic milieu of Mystra.
The stemma codicum drawn up by Müller (Würzburger Jahrbücher für die Altertumswissenschaft 5: 237–251, 1979) can thus be understood in its deeper cultural meaning, i.e. as an outline enabling us to understand how the philosopher propagated his ideas and to follow where and how they were received.
Assessing Trends in Practice Demographics of Underrepresented Minority Pediatricians, 1993–2007
Authors: Basco William T. , Cull William L. , O'Connor Karen G. , Shipman Scott A. 
Published: February 2010

OBJECTIVE:To assess whether underrepresented minority (URM) pediatricians serve minority and/or publicly insured or uninsured children to a greater degree than non-URM pediatricians, and to evaluate trends in these relationships.PARTICIPANTS AND METHODS:Respondents to American Academy of Pediatrics surveys in 1993, 2000, and 2007, provided their race/ethnicity, practice locations, and estimated race/ethnicity and insurance sources of their patient panels. We classified pediatricians by race/ethnicity as either URM (black, Hispanic, Hawaiian/Pacific Islander, or American Indian/Alaskan Native) or non-URM (white, non-Hispanic/Latino, Asian, or other). We compared the average percentages of minority individuals (excluding Asians) in the patient panels of URM and non-URM pediatricians, and compared the average percentages of publicly insured (includes TRICARE) or uninsured patients.RESULTS:Response rates were &gt;50% for all surveys. There were 1003 (10.2% URM) postresidency respondents in 1993, 707 (11.8% URM) in 2000, and 900 (11.1% URM) in 2007. In all 3 surveys, the average percentage of minority children in URM pediatricians' patient panels was higher than for non-URM pediatricians by approximately 20 percentage points (all P &lt; .001). The differences in the percentages of patients who were either publicly insured or uninsured widened over the study period, from 46% in URM pediatric practices versus 38.8% in non-URM practices in 1993 to 59.7% vs 40.7%, respectively, in 2007 (P &lt; .001). In multivariable analyses, URM pediatricians' patient panels had a higher mean percentage of minorities (15.2 percentage points greater; 95% confidence interval [CI]: 12.1–18.4) and a higher mean percentage of publicly insured and uninsured patients (10.9 percentage points greater; 95% CI: 6.7–15.4) compared with non-URM pediatricians' patient panels.CONCLUSIONS:Over the last 14 years, URM pediatricians were more likely than their non-URM peers to care for minority children and publicly insured or uninsured patients. This relationship has not appeared to attenuate over time, and these data support ongoing and enhanced efforts to recruit qualified URMs into pediatric careers to meet the growing needs of the expanding minority child population.
A BIOMECHANICAL VALIDATION OF A NEW FEMORAL NECK FIXATION DYNAMIC HIP SCREW FOR PROXIMAL FEMORAL FRACTURE
Authors: Lin Shih-Wei , Wang Jaw-Lin 
Published: February 2010

High failure rates are expected in the treatment of osteoporotic proximal femoral fractures. A newly designed femoral neck locking dynamic hip screw has been developed to increase the fixation strength; a biomechanical examination was performed to prove its efficacy. Femoral surrogate specimens were used for the test. Unstable intertrochanteric fractures were created on specimens. Then these specimens were divided into two groups to test two different methods of fixation: (1) the conventional dynamic hip screw and (2) the new designed femoral neck fixation dynamic hip screw. For each specimen, the peak cyclic loading was 800 N, and a total of 20,000 cycles were applied. The vertical displacement, rotation around the long axis of lag screw, and the varus rotation around the center of femoral head between the two groups were compared at specific intervals. All the conventional dynamic hip screw constructs failed within 1000 cycles, while no gross mechanical failure was recorded for the femoral neck fixation dynamic hip construct even after 20,000 loading cycles. The mechanical test comparing the two constructs at the end of each 1000 loading cycles demonstrated that the femoral neck fixation dynamic hip screw construct is stronger than that of the conventional dynamic hip screw. For the fixation of proximal femoral fractures, the femoral neck fixation dynamic hip screw can provide a stronger support than what a conventional dynamic hip screw can do. At the same time, femoral neck can be a suitable site for the application of proximal locking screws.
One‐year change in radiographic joint space width in patients with unilateral joint space narrowing: Data from the osteoarthritis initiative
Authors: Benichou O. D. , Hunter D. J. , Nelson D. R. , Guermazi A. , Eckstein F. , Kwoh K. , Myers S. L. , Wirth W. , Duryea J. 
Published: February 2010

AbstractObjectiveTo examine the rate of joint space width (JSW) loss in both knees of patients with unilateral medial joint space narrowing (JSN) at baseline.MethodsCases were selected from a pool of 2,678 subjects enrolled in the Osteoarthritis Initiative cohort. Inclusion criteria for the present study were unilateral medial JSN, bilateral frequent knee pain, and body mass index (BMI) ≥25 kg/m2. Baseline and 1‐year fixed flexion radiographs of both knees were read (blinded to time point) using an automated algorithm for minimum JSW and JSW at 4 fixed locations in the medial compartment.ResultsSixty‐seven participants met the inclusion criteria: 43 women and 24 men, with mean ± SD age 60 ± 9 years and mean ± SD BMI 31 ± 4 kg/m2. Thirty‐seven subjects (55%) had ≥1 definite tibiofemoral osteophyte. The average progression in no‐JSN knees was comparable with that in JSN knees (approximately −0.2 mm/year). However, JSW change was more variable in no‐JSN knees, resulting in standardized response means (SRMs; the mean/SD) of approximately −0.24 in no‐JSN knees versus approximately −0.41 in JSN knees on average at the 4 fixed locations, and SRMs of −0.24 and −0.35, respectively, for minimum JSW. Young age and high BMI were associated with increased progression, especially in JSN knees.ConclusionJSN and no‐JSN knees progressed at a comparable rate, but a wider distribution of JSW change in no‐JSN knees resulted in a poorer sensitivity to change in these knees.
Osteoporosis screening, prevention, and treatment in systemic lupus erythematosus: application of the systemic lupus erythematosus quality indicators
Authors: Schmajuk Gabriela , Yelin Edward , Chakravarty Eliza , Nelson Lorene M. , Panopolis Pantelis , Yazdany Jinoos 
Published: February 2010

AbstractObjectiveOsteoporosis and fragility fractures are associated with significant morbidity for patients with systemic lupus erythematosus (SLE). New quality indicators (QIs) for SLE advise bone mineral density testing, calcium and vitamin D use, and antiresorptive or anabolic treatment for specific subgroups of patients receiving high‐dose steroids.MethodsSubjects were participants in the University of California, San Francisco Lupus Outcomes Study, an ongoing longitudinal study of patients with physician‐confirmed SLE, in 2007–2008. Patients responded to an annual telephone survey and were queried regarding demographic, clinical, and other health care–related variables. Multiple logistic regression was used to predict receipt of care per the QIs described above.ResultsOne hundred twenty‐seven patients met the criteria for the formal definitions of the denominators for QI I (screening) and QI II (calcium and vitamin D); 91 met the formal criteria for QI III (treatment). The proportions of patients receiving care consistent with the QIs were 74%, 58%, and 56% for QIs I, II, and III, respectively. In a sensitivity analysis of all steroid users (n = 427 for QI I and II and n = 224 for QI III), rates were slightly lower. Predictors of receiving care varied by QI and by denominator; however, female sex, older age, white race, and longer disease duration were associated with higher‐quality care.ConclusionBone health–related care in this community‐based cohort of SLE patients is suboptimal. Quality improvement efforts should address osteoporosis prevention and care among all SLE patients, especially those receiving high‐dose, prolonged steroids.
An Expeditious Route to Fluorinated Rapamycin Analogues by Utilising Mutasynthesis
Authors: Goss Rebecca J. M. , Lanceron Simon , Deb Roy Abhijeet , Sprague Simon , Nur‐e‐Alam Mohammed , Hughes David L. , Wilkinson Barrie , Moss Steven J. 
Published: February 2010

AbstractRapamycin is a drug with several important clinical uses. Its complex structure means that total synthesis of this natural product and its analogues is demanding and lengthy. A more expeditious approach is to utilise biosynthesis to enable the generation of otherwise synthetically intractable analogues. In order to achieve this, rules governing biosynthetic precursor substrate preference must be established. Through determining these rules and synthesising and administering suitable substrate precursors, we demonstrate the first generation of fluorinated rapamycin analogues. Here we report the generation of six new fluororapamycins.
Surface Layer‐by‐Layer Chemical Deposition Reaction for Nanosized Thin‐Film Formation of Metal Complexes of 2‐Mercaptonicotinic Acid
Authors: Haggag Sawsan M. S. 
Published: February 2010

Abstract2‐Mercaptonicotinic acid [H2mna] reacted with MnII, CoII, NiII, CuII, and ZnII by using a layer‐by‐layer chemical deposition technique; thin‐film nanosized metal–[Hmna]2 complexes were formed. The metal complexes were synthesized by the alternative dipping of a glass substrate into the metal ion solution followed by the ligand solution. A molar stoichiometric ratio of 1:2 was characterized for all newly synthesized nanosized MnII‐, CoII‐, NiII‐, CuII‐, and ZnII–2‐mercaptonicotinate complexes, as confirmed from analysis of the metal. Electron impact mass spectrometry (EIMS) of the collected particles from the thin‐film deposited MnII[Hmna]2 complex (as a selected example) indicates molecular ion peaks at m/z values of 155 and 363 amu for [H2mna] and MnII[Hmna]2, respectively. The deposited thin films of the nanosized metal complexes were subjected to analysis and imaging by scanning electron microscopy (SEM) and were identified to give a range of detected particle sizes ≥20–130 nm. The five metal–[Hmna]2 complexes were characterized by FTIR spectroscopy, and the ligand was found to bind to the metal through the carboxylic oxygen atom and the mercapto sulfur atom. The UV/Vis spectra of the deposited thin film materials and of the ethanol solutions of the complexes were recorded to identify the possibility of d–d transitions in all newly synthesized metal–[Hmna]2 complexes. Thermal gravimetric analysis (TGA and DTG) was also used to identify the possible thermal degradation processes and to calculate some thermodynamic parameters.