bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Authors: Hahn Matthew W 
Published: July 2007

Abstract
Background
Comparative genomic studies are revealing frequent gains and losses of whole genes via duplication and pseudogenization. One commonly used method for inferring the number and timing of gene gains and losses reconciles the gene tree for each gene family with the species tree of the taxa considered. Recent studies using this approach have found a large number of ancient duplications and recent losses among vertebrate genomes.

Results
I show that tree reconciliation methods are biased when the inferred gene tree is not correct. This bias places duplicates towards the root of the tree and losses towards the tips of the tree. I demonstrate that this bias is present when tree reconciliation is conducted on both multiple mammal and Drosophila genomes, and that lower bootstrap cut-off values on gene trees lead to more extreme bias. I also suggest a method for dealing with reconciliation bias, although this method only corrects for the number of gene gains on some branches of the species tree.

Conclusion
Based on the results presented, it is likely that most tree reconciliation analyses show biases, unless the gene trees used are exceptionally well-resolved and well-supported. These results cast doubt upon previous conclusions that vertebrate genome history has been marked by many ancient duplications and many recent gene losses.
Living With Prostate Cancer: Patients' and Spouses' Psychosocial Status and Quality of Life
Authors: Northouse Laurel L. , Mood Darlene W. , Montie James E. , Sandler Howard M. , Forman Jeffrey D. , Hussain Maha , Pienta Kenneth J. , Smith David C. , Sanda Martin G. , Kershaw Trace 
Published: July 2007

Purpose Despite the high prevalence of prostate cancer, little information is available on the quality of life of men and their spouses during the phases of illness. This study assessed patients' and spouses' quality of life, appraisal of illness, resources, symptoms, and risk for distress across three phases of prostate cancer: newly diagnosed, biochemical recurrence, and advanced. Patients and Methods The sample consisted of 263 patient/spouse dyads. A stress-appraisal conceptual model guided the selection of variables which were then assessed with established instruments. Study variables were examined for phase effects (differences in dyads across three phases), role effects (patients v spouses), and phase-by-role interactions (differences within dyads across phases) using analysis of variance (ANOVA). Results More phase effects than role effects were found, indicating that the psychosocial experiences of patients and their spouses were similar, but differed from dyads in other phases. Dyads in the advanced phase were at highest risk for distress. These patients had the lowest physical quality of life, and their spouses had the lowest emotional quality of life of all participants. Dyads in the biochemical recurrence and advanced phases had more negative appraisals of illness and caregiving, greater uncertainty, and more hopelessness compared with dyads in the newly diagnosed phase. Spouses, in contrast to patients, had less confidence in their ability to manage the illness and perceived less support across all phases of illness. Conclusion Phase-specific programs of care are needed to assist both men with prostate cancer and their spouses to manage the effects of illness.
Oral Contraceptives and Breast Cancer Risk in the International BRCA1/2 Carrier Cohort Study: A Report From EMBRACE, GENEPSO, GEO-HEBON, and the IBCCS Collaborating Group
Authors: Brohet Richard M. , Goldgar David E. , Easton Douglas F. , Antoniou Antonis C. , Andrieu Nadine , Chang-Claude Jenny , Peock Susan , Eeles Rosalind A. , Cook Margaret , Chu Carol , Noguès Catherine , Lasset Christine , Berthet Pascaline , Meijers-Heijboer Hanne , Gerdes Anne-Marie , Olsson Håkan , Caldes Trinidad , van Leeuwen Flora E. , Rookus Matti A. 
Published: July 2007

Purpose Earlier studies have shown that endogenous gonadal hormones play an important role in the etiology of breast cancer among BRCA1/2 mutation carriers. So far, little is known about the safety of exogenous hormonal use in mutation carriers. In this study, we examined the association between oral contraceptive use and risk of breast cancer among BRCA1/2 carriers. Patients and Methods In the International BRCA1/2 Carrier Cohort study (IBCCS), a retrospective cohort of 1,593 BRCA1/2 mutation carriers was analyzed with a weighted Cox regression analysis. Results We found an increased risk of breast cancer for BRCA1/2 mutation carriers who ever used oral contraceptives (adjusted hazard ratio [HR] = 1.47; 95% CI, 1.16 to 1.87). HRs did not vary according to time since stopping use, age at start, or calendar year at start. However, a longer duration of use, especially before first full-term pregnancy, was associated with an increased risk of breast cancer for both BRCA1 and BRCA2 mutation carriers (4 or more years of use before first full-term pregnancy: HR = 1.49 [95% CI, 1.05 to 2.11] for BRCA1 carriers and HR = 2.58 [95% CI, 1.21 to 5.49] for BRCA2 carriers). Conclusion No evidence was found among BRCA1/2 mutation carriers that current use of oral contraceptives is associated with risk of breast cancer more strongly than is past use, as is found in the general population. However, duration of use, especially before first full-term pregnancy, may be associated with an increasing risk of breast cancer among both BRCA1 and BRCA2 mutation carriers.
Notes from the Laboratories of Democracy: State Government Enactments of Market and State-Based Health Insurance Reforms in the 1990s
Authors: Barrilleaux Charles , Brace Paul 
Published: July 2007

We identify two policy strategies that state governments pursue to reduce uninsurance, and we classify policies as being either state based or market based. The two policy strategies are distinguished by whether states rely on the institutional capabilities of the state or market processes to provide insurance. We develop and test models to explain states' adoptions of each type of policy. Using Poisson regression, we evaluate hypotheses suggested by the two strategies with data from U.S. states in the 1990s. The results indicate that institutionally more-capable state governments with strong liberal-party presence in the legislature adopt more state-based policies and fewer market-based policies. By contrast, the model of market-based, business-targeted reforms reveals that government capability plays a smaller role. Instead, these policies are driven by economic affluence, political competition, higher incomes, greater uninsurance, and more previous attempts to address the uninsurance problem.These findings reveal distinct institutional, partisan, electoral and demographic influences that shape state-based and market-based strategies. First, policy choices can be driven by the presence or absence of state capability. The domain of feasible policy choices open to states with institutional capability may be decidedly different than that available to states with fewer institutional resources. Second, while market-based policy approaches may be the most feasible politically, they may be the least successful in remedying practical uninsurance issues. These results thus reveal that institutional characteristics of states create an important foundation for policy choice and policy success or failure. These results would suggest that the national government's strategy of pursuing market-based solutions to the problem will not result in its being solved.
Hot isostatic pressing for the enhancement of copper dies incorporating a thermally sprayed protective layer
Authors: Kamara A M , Davey K 
Published: July 2007

Recent efforts have considered the feasibility of using copper dies protected with a thermally sprayed coating layer in pressure die casting processes. Although such dies offer considerable advantage over traditional designs, particularly improved processing times, a particular drawback is the poor quality of the deposited layer. The coating layer of wearresistant material, which can be deposited on to a die-cavity surface using an arc-wire thermalspray process, can exhibit undesirable porosity, cracks, and inclusions. This in turn can result in poor in-service performance with castings of poor surface quality or dies with a reduced life. As a route to identifying a suitable and effective coating treatment strategy to enhance coating performance on the die, the current paper presents work carried out to investigate the effectiveness of the hot isostatic pressing (HIP) process towards the healing of porosity (i.e. coating densification) in chrome-steel coating and the enhancement of its hardness and bond strength on chrome-copper substrates. The results of the investigation reveal significant improvement in coating densification and bond strength at all process conditions. Also investigated is the relationship between bond strength, densification, and HIP temperatures. The HIP process is also shown to reduce coating hardness to levels of hardness equivalent to that of traditional tool steel. On the whole, the investigation suggests that optimum performance could be achieved from chrome-steel coating on chrome-copper substrates if HIPped at a temperature of 925°C and a pressure of 100 MPa.
Alternate methods for sampling in coordinate metrology
Authors: Collins C E , Fay E B , Aguirre-Cruz J A , Raman S 
Published: July 2007

A variety of inspection equipment exists in industry to capture the points on a surface that will envisage manufacturing form errors. Manufacturing inspection faces a problem of finding optimal methods to capture an evenly spread distribution of points on the surface. Sampling does not yield complete information about a surface. Each material removal process leaves a unique pattern on the surface of the workpiece, which has to be taken into consideration while developing the sampling strategy. For instance, round patterns left by face milling at low feeds on flat surfaces, and spiral patterns left during surface milling and turning operations on surfaces of revolution. Two new methods have been developed to improve sampling using the coordinate measuring machine (CMM) for inspection of flat and revolved surfaces. These are the Spiral, and Hamspi sampling methods. The Spiral method focuses on the centre of the area and uses the Archimedean spiral. Hamspi is a method that combines both the Spiral and randomized Hammersley to measure points in the middle as well as the outer zone of the workpiece. Mathematical comparisons of these methods have been made to establish feasibility. An experiment was performed to determine the accuracy of these models using two dependent variables: inspection time and minimum zone. The minimum zone was (statistically) significantly affected by only two factors: sample size and workpiece shape. The sampling time was however affected by sample size, workpiece shape, and the interaction between them. This study observed that the beginning and ending cutting zones of spherical surfaces were the most significant regions to verify. It was found that the Spiral and Hamspi methods had similar point distributions as the Hammersley method while placing more emphasis on the origin of the workpiece.
Preparation of Pillared Carbons by Pyrolysis of Silylated Graphite Oxide
Authors: Matsuo Yoshiaki , Sakai Yoshimasa , Fukutsuka Tomokazu , Sugie Yosohiro 
Published: July 2007

Abstract
Pillared carbons containing silica between their carbon layers were first prepared by the pyrolysis of graphite oxide silylated by 3-aminopropyldiethoxymethylsilane between 450 and 550 °C under vacuum. They possessed both microporosities and mesoporosities existing between their carbon layers.
Review essay: Reassessing anthropology's maverick: The archaeological fieldwork of Frank Hamilton Cushing
Authors: PAREZO NANCY J. 
Published: July 2007

The Lost Itinerary of Frank Hamilton Cushing. Volume two of Frank Hamilton Cushing and the Hemenway Southwestern Archaeological Expedition, 1886–1889. Curtis M. Hinsley and David R. Wilcox, eds. Tucson: University of Arizona Press, 2002. xxxvi + 349 pp., illustrations, notes, bibliography, index.The Lost Florida Manuscript of Frank Hamilton Cushing. Phyllis E. Kolianos and Brent R. Weisman, eds. Gainesville: University Press of Florida, 2005. xiv + 281 pp., illustrations, appendixes, notes, bibliography, index.The Florida Journals of Frank Hamilton Cushing. Phyllis E. Kolianos and Brent R. Weisman, eds. Gainesville: University Press of Florida, 2005. xv + 161 pp., notes, illustrations, bibliography, index.Anthropology has had many charismatic figures in its past whose work has bordered on genius and who have presaged contemporary anthropological theories, issues, the choice of research topics, methodologies, or ethical concerns. Although often marginalized in the history of anthropology, a few of these key individuals have captured our imagination and recent attention because long‐lost diaries, field notes, and reports have come to light, often after years of diligent searching by dedicated scholars. This review article assesses the contributions of three recent books on one of American anthropology's most fascinating and enigmatic individuals: Frank Hamilton Cushing. These works focus on Cushing's groundbreaking regional research in the American Southeast (Florida) and the Southwest (Arizona) and tell us much about the foundational values of our discipline.
Family History Predicts Stress Fracture in Active Female Adolescents
Authors: Loud Keith J. , Micheli Lyle J. , Bristol Stephanie , Austin S.Bryn , Gordon Catherine M. 
Published: July 2007

OBJECTIVE. Increased physical activity and menstrual irregularity have been associated with increased risk for stress fracture among adult women active in athletics. The purposes of this study were to determine whether menstrual irregularity is also a risk factor for stress fracture in active female adolescents and to estimate the quantity of exercise associated with an increased risk for this injury.
PATIENTS AND METHODS. A case-control study was conducted of 13- to 22-year-old females diagnosed with their first stress fracture, each matched prospectively on age and self-reported ethnicity with 2 controls. Patients with chronic illnesses or use of medications known to affect bone mineral density were excluded, including use of hormonal preparations that could alter menstrual cycles. The primary outcome, stress fracture in any extremity or the spine, was confirmed radiographically. Girls with stress fracture had bone mineral density measured at the lumbar spine by dual-energy x-ray absorptiometry.
RESULTS. The mean ± SD age of the 168 participants was 15.9 ± 2.1 years; 91.7% were postmenarchal, with a mean age at menarche of 13.1 ± 1.1 years. The prevalence of menstrual irregularity was similar among cases and controls. There was no significant difference in the mean hours per week of total physical activity between girls in this sample with stress fracture (8.2 hours/week) and those without (7.4 hours/week). In multivariate models, case subjects had nearly 3 times the odds of having a family member with osteoporosis or osteopenia. In secondary analyses, participants with stress fracture had a low mean spinal bone mineral density for their age.
CONCLUSIONS. Among highly active female adolescents, only family history was independently associated with stress fracture. The magnitude of this association suggests that further investigations of inheritable skeletal factors are warranted in this population, along with evaluation of bone mineral density in girls with stress fracture.
Decision-Making for Postpartum Discharge of 4300 Mothers and Their Healthy Infants: The Life Around Newborn Discharge Study
Authors: Bernstein Henry H. , Spino Cathie , Finch Stacia , Wasserman Richard , Slora Eric , Lalama Christina , Touloukian Carol Litten , Lilienfeld Harris , McCormick Marie C. 
Published: July 2007

OBJECTIVES. Postpartum discharge of mothers and infants who are not medically or psychosocially ready may place the family at risk. Most studies of postpartum length of stay, however, do not reflect the necessary complexity of decision-making. With this study we aimed to characterize decision-making on the day of postpartum discharge from the perspective of multiple key informants and identify correlates of maternal and newborn unreadiness for discharge.PATIENTS AND METHODS. This was a prospective observational cohort study of healthy term infants with mothers, pediatric providers, and obstetricians as key informants to assess the decision-making process regarding mother-infant dyad unreadiness for discharge. A mother-infant dyad was defined as unready for postpartum hospital discharge if ≥1 of 3 informants perceived that either the mother or infant should stay longer at time of nursery discharge. Data were collected through self-administered questionnaires on the day of discharge.RESULTS. Of 4300 mother-infant dyads, unreadiness was identified in 17% as determined by the mother (11%), pediatrician (5%), obstetrician (1%), and ≥2 informants (&lt;1%). Significant correlates of unreadiness were as follows: black non-Hispanic maternal race/ethnicity, maternal history of chronic disease, primigravid status, inadequate prenatal care as determined by the Kotelchuck Adequacy of Prenatal Care Utilization Index, delivering during nonroutine hours, in-hospital neonatal problems, receiving a limited number of in-hospital classes, and intent to breastfeed.CONCLUSIONS. Mothers, pediatricians, and obstetricians must make decisions about postpartum discharge jointly, because perceptions of unreadiness often differ. Sensitivity toward specific maternal vulnerabilities and an emphasis on perinatal education to insure individualized discharge plans may increase readiness and determine optimal timing for discharge and follow-up care.
Pore classification in the characterization of porous materials: A perspective
Authors: Zdravkov Borislav , Čermák Jiří , Šefara Martin , Janků Josef 
Published: July 2007

AbstractThe original version of the article was published in Cent. Eur. J. Chem., Vol. 5(2), (2007), pp. 385–395. It can be also found online at: http://dx.doi.org/10.2478/s11532-007-0017-9.Unfortunately, the original version of this article contains mistakes in the Acknowledgements section. There should be: This work was supported by Grants 240/08/0016 of Institute of Chemical Technology, 257 Prague, 104/06/1079 of Czech Science Foundation and MSM6046137308 of Ministry of Education, Youth and Sports of the Czech Republic.
Dirac and Yang monopoles revisited
Authors: Meng Guowu 
Published: July 2007

AbstractThe Dirac monopoles in 3-space and their generalization by C.N. Yang to 5-space are observed to be just the Levi-Civita spin connections of the cylindrical Riemannian metric on the 3-and 5-dimensional punctured spaces respectively. Their straightforward generalization to higher dimensions is also investigated.
A remark about possible unity of the neutron star and black hole high frequency QPOs
Authors: Török Gabriel , Stuchlík Zdeněk , Bakala Pavel 
Published: July 2007

AbstractIn a series of papers it was discussed,on the basis of phenomenological arguments, whether the high frequency quasiperiodic oscillations (kHz QPOs)observed in the neutron-star and black-hole X-ray sources originate in the same physical mechanism. Recently it was suggested that a general trend seen in neutron star kHz QPOs instead excludes such a uniform origin. Using the example of the atoll source 4U 1636-53 we illustrate that this is not neccesarily true.
Variation in the analgesic activity of opioid peptide fragments in correlation with the amino acidic sequence
Authors: Jaba Irina , Tamba Bogdan , Manolidis Georgios , Mungiu Ostin 
Published: July 2007

Abstract
Short fragments of typical or atypical opioid peptides, lacking the whole four amino acid sequence of the enkephalin motif, can preserve a significant percentage of the analgesic activity of the original peptides. This paper investigates the importance of the amino-acidic sequence of minimum structure typical opioid peptides for the analgesic activity. Different groups of rats were treated with 1) Gly-Tyr, 0.5 mg/rat i.t., 2) Tyr-Gly, 0.5 mg/rat i.t., 3) Tyr-Gly-Gly, 0.5 mg/rat i.t., 4) Gly-Gly-Phe-Leu, 0.5 mg/rat i.t., 5) Leu-enkephalin, 0.5 mg/rat i.t.. The analgesic effect of the tested substances was appreciated through the nociceptive threshold for thermal (plantar test) and mechanical nociception (algesimetric test). Fragments of typical opioid peptides elicited antinociceptive activity only when a tyrosine residue was present at the N-terminal end of the amino-acidic sequence. The presence of Nterminal tyrosine provides affinity for the opioid receptors and significant analgesic activity. The intensity of the antinociceptive effect was directly proportional with the length of the amino-acidic sequence. The inhibition of the analgesic effect by previous administration of naloxone proves that this effect is mediated through the opioid system.
Object extraction as a basic process for content-based image retrieval (CBIR) system
Authors: Jaworska T. 
Published: July 2007

AbstractThis article describes the way in which image is prepared for content-based image retrieval system. Automated image extraction is crucial; especially, if we take into consideration the fact that the feature selection is still a task performed by human domain experts and represents a major stumbling block in the process of creating fully autonomous CBIR systems. Our CBIR system is dedicated to support estate agents. In the database, there are images of houses and bungalows. We put all our efforts into extracting elements from an image and finding their characteristic features in the unsupervised way. Hence, the paper presents segmentation algorithm based on a pixel colour in RGB colour space. Next, it presents the method of object extraction applied to obtain separate objects prepared for the process of introducing them into database and further recognition. Moreover, we present a novel method of texture identification which is based on wavelet transformation. Due to the fact that the majority of texture is geometrical (such as bricks and tiles) we have used the Haar wavelet. After a set of low-level features for all objects is computed, the database is stored with these features.
Stabilization of Palladium Nanoparticles by Polyoxometalates Appended with Alkylthiol Tethers and their Use as Binary Catalysts for Liquid Phase Aerobic Oxydehydrogenation
Authors: De bruyn Mario , Neumann Ronny 
Published: July 2007

AbstractA polyoxometalate with two alkyl thiol appendages, Q4[SiW11O40(SiCH2CH2CH2SH)2] (Q=ammonium salt) stabilized the formation of palladium nanoparticles. This tethered polyoxometalate–palladium binary catalyst was effective for the aerobic oxydehydrogenation of vinylcyclohexene and vinylcyclohexane to styrene as the major product via activation of the allylic, tertiary carbon‐hydrogen bond.
Synthesis of Polymer‐Supported Fesulphos Ligands and their Application in Asymmetric Catalysis
Authors: Martín‐Matute Belén , Pereira Susana Isabel , Peña‐Cabrera Eduardo , Adrio Javier , Silva Artur M. S. , Carretero Juan C. 
Published: July 2007

AbstractThe synthesis of two Fesulphos‐based chiral ligands and their immobilization on a polystyrene support is described. These supported chiral ligands act as very efficient catalysts in 1,3‐dipolar cycloaddition and allylic substitution reactions providing the products with excellent enantioselectivities (91 to >99 % ee). Filtration of the catalyst from the reaction mixtures allows simple product isolation. The polymer‐supported Cu complex of chiral ligand PS‐8 can be recycled without further addition of a copper salt in 1,3‐dipolar cycloaddition reactions.