bluuebunny/crossref_metadata_2025 huggingface dataset:
Speciation in the New Millennium: What's Left to Know?
Authors: Noor Mohamed A.F. , Coyne Jerry A.
Published: October 2008

The last few decades have seen a surge of interest in speciation, the genetic changes underlying it, and the evolutionary forces driving it. As with most disciplines, however, the nature of the questions addressed has changed with time. Many studies from the 1980s and 1990s often asked questions about whether certain processeseveroccur in nature (e.g., speciation with gene flow). Since that time, case studies have provided evidence that nearly all evolutionary processes thought to be involved in speciation have occurred at least once. As a result, we are now in a new era where the "big questions" must go beyond demonstrations that a phenomenon has happened at least once. Here we discuss a few open questions in speciation—questions that we feel are not only exciting but tractable. We focus our discussion most sharply on recent studies inDrosophilaand related species, the area of our expertise. However, we also emphasize the importance of broad taxonomic meta-analyses testing the importance or frequency of various processes thought to cause speciation.
Lateral Transfer: A Survey and New Developments
Authors: Snir Sagi
Published: October 2008

Exponentially accumulating genetic molecular data were supposed to bring us closer to resolving one of the most fundamental issues in biology—the reconstruction of the tree of life. This tree should encompass the evolutionary history of all living creatures on earth and trace back a few billions of years to
the most ancient microbial ancestor.

Ironically, this abundance of data only blurs our traditional beliefs and seems to make this goal harder to achieve than initially thought. This is largelydue to lateral gene transfer, the passage of genetic material between organisms not through lineal descent. Evolution in light of lateral transfer tangles the traditional universal tree of life, turning it into a network of relationships. Lateral
transfer is a significant factor in microbial evolution and is the mechanism of antibiotic resistance spread in bacteria species.

In this paper we survey current methods designed to cope with lateral transfer in conjunction with vertical inheritance. We distinguish between phylogenetic-based methods and sequence-based methods and illuminate the advantages and disadvantages of each. Finally, we sketch a new statistically rigorous approach aimed at identifying lateral transfer between two genomes.
Heparin‐Dependent Antibodies and Thrombosis without Heparin‐Induced Thrombocytopenia
Authors: Bream‐Rouwenhorst Heather R. , Hobbs Ryan A.
Published: October 2008

Although heparin‐dependent antibodies (HDAs) typically manifest with thrombocytopenia as in heparin‐induced thrombocytopenia (HIT), they may also manifest with preserved platelet counts. We describe a 35‐year‐old woman who developed severe thrombotic complications due to heparinization and unrecognized HDAs. She had received subcutaneous heparin as prophylaxis for deep vein thrombosis during a 5‐day hospitalization for postpartum cardiomyopathy. Five days after discharge (day 1), she developed bilateral lower extremity arterial thrombi and underwent heparinization and successful lower extremity thrombectomies. A pulmonary embolus and hepatic and renal infarcts were then found. On days 2–6, the patient experienced a myocardial infarction, ischemic cerebrovascular accident, recurrent lower extremity arterial thrombus, and splenic infarct. On day 7, blood obtained on day 4 was found to be strongly positive for HDAs. In the interim, the patient had been transitioned to warfarin. Her platelet counts were never less than 75% of baseline and were consistently above 200 times 103/mm3. Hypercoagulability studies were negative. The patient's score on the Naranjo adverse drug reaction probability scale indicated that the relationship between this adverse reaction and heparin was probable. An extensive MEDLINE search located 22 other reports of patients who developed HDAs, sometimes associated with thrombosis, but whose platelet counts did not decrease. As with our patient, many of these case reports described clinicians who overlooked thrombosis due to HDAs because the patients did not have HIT. Clinicians should be cognizant of this possibility and consider a diagnosis of HDAs in patients with ongoing thrombosis who are receiving heparin therapy. It is strongly recommended that heparin be substituted with another anticoagulant in such cases until the presence of HDAs can be definitively ruled out.
Successful Use and Dosing of Bivalirudin After Temporary Total Artificial Heart Implantation: A Case Series
Authors: Crouch Michael A. , Kasirajan Vigeshwar , Cahoon William , Katlaps Gundars J. , Gunnerson Kyle J.
Published: October 2008

The temporary total artificial heart (TAH‐t) has emerged as an effective bridge to transplantation for individuals with biventricular failure. Implantation of a TAH‐t creates a hypercoagulable state requiring a multidrug approach that includes low‐dose unfractionated heparin (UFH) in order to minimize thromboembolism. A concern with UFH is the development of heparin‐dependent antibodies, which develop in up to 50% of patients receiving the drug as part of cardiopulmonary bypass. If UFH therapy continues postoperatively, the risk of heparin‐induced thrombocytopenia approaches 3%. Small investigations have demonstrated that bivalirudin, given as a bolus of 0.75–1 mg/kg followed by an infusion at 1.75‐2.5 mg/kg/hour, is an effective alternative to UFH for therapeutic anticoagulation during coronary artery bypass surgery, valve replacement, or both. We describe a series of five adults (age range 24–58 yrs) who received bivalirudin as an alternative to low‐dose UFH after TAH‐t implantation. None of the patients had documented heparin‐induced thrombocytopenia. Treatment was started at the discretion of the treating physician, and adjustments were based principally on the results of thromboelastography. Additional general monitoring included activated partial thromboplastin time, prothrombin time, international normalized ratio, fibrinogen, D‐dimer, platelet count, hemoglobin, hematocrit, and platelet aggregation studies. Bivalirudin therapy was continued until successful warfarin implementation. All five patients received bivalirudin in addition to standard antithrombotic therapy. Bivalirudin treatment started at a dosage of 0.005 or 0.01 mg/kg/hour with titration to maintain normocoagulability, which occurred (without concomitant warfarin therapy) within the dosage range of 0.01‐0.02 mg/kg/hour. Duration of TAH‐t implantation was a mean of 38.8 days (range 25–60 days), and bivalirudin was continued for a mean of 15.2 days (range 7–24 days). No major hemorrhagic events occurred during treatment, and all patients successfully transitioned to warfarin therapy. Low‐dose bivalirudin, as an alternative to UFH, maintained normocoagulability after TAH‐t implantation. Further investigation is warranted to define the role and dosing of bivalirudin in this situation.
Ethical Issues Related to Clinical, Translational, and Health System Research
Authors: Klepser Michael E. , Matzke Gary R. , Vivian Eva , Granberry Mark , Majerus Thomas , Wiggins Barbara , Hill‐Zabala Christina , Weimert Nicole , Raebel Marsha A.
Published: October 2008

In 2005, a charge was created to update the the American College of Clinical Pharmacy's 1993 white paper on Ethical Issues in Clinical Pharmacy Research. In that paper, emerging threats to scientific integrity were identified, and guidance was provided to investigators to minimize their risk for impropriety. The committee charged with this task considered a variety of issues pertaining to research, including those that are related to patients, pharmacogenomics, economics, and study design and oversight. Objectivity and integrity are the foundations on which all researchers should base their scientific endeavors. One's desire for acclaim, promotion, or financial reward must be closely monitored so that these factors do not impair a researcher's judgment and objectivity. The ethical line can become easily blurred. Therefore, the constructs of scientific integrity should be integral to pharmacy education and scientific training programs, and their principles applied throughout one's career.
Foraging Shorebird Response to Trail Use Around San Francisco Bay
Authors: TRULIO LYNNE A. , SOKALE JANA
Published: October 2008

Abstract: We studied how human use of trails affected foraging shorebirds over 24 months at 3 locations around San Francisco Bay, California, USA. By observing sites with trails and nearby sites without trails, we assessed whether numbers of trail users had an effect on the number of birds, species richness, or proportion of shorebirds foraging on tidal mudflats. Human use at non‐trail sites averaged <1 person/hour, whereas use at trail sites averaged 68 people/hour. Despite these differences, we found no negative effects of trail use on the number of birds, species richness, or proportion of birds foraging, either overall or by season, when comparing trail to non‐trail sites. Human use of trail sites on higher use days (typically weekends) averaged about 2.5 times the level on lower use days (typically weekdays). When comparing bird response on paired lower and higher use days at the trail sites, we found the number of shorebirds decreased with increasing trail use (F1,119 = 4.20, P = 0.043), with higher trail‐use days averaging 25% fewer birds than on lower use days. Although managers may allow human use of trails adjacent to shorebird foraging areas under some conditions, high levels of trail use may negatively affect birds, making it essential to offer birds alternative, trail‐free foraging opportunities.
Methods of Predicting Risks of Wheat Damage by White‐Fronted Geese
Authors: AMANO TATSUYA , USHIYAMA KATSUMI , HIGUCHI HIROYOSHI
Published: October 2008

Abstract: Accurately predicting occurrence of wildlife damage is crucial for effective management of problematic wildlife species, because accurate predication allows deterrence efforts to be focused at sites or times where damage is most likely. We explored methods to predict occurrence of white‐fronted geese (Anser albifrons) grazing in wheat fields around Lake Miyajimanuma, Japan. Depletion of waste rice grains caused geese to forage on wheat leaves in spring, reducing wheat harvest in grazed fields. The cumulative number of goose‐days per hectare of rice‐planted area from the beginning of the staging period explained the variation in the proportion of geese foraging in wheat fields. A logistic regression model on the location of vulnerable fields showed that goose grazing was likely to occur in wheat fields far from roads and windbreaks and those close to (within 1,000–2,000 m of) previously grazed fields. Although probability of occurrence of goose grazing was initially low in wheat fields with scaring devices, effectiveness of such devices was lost over the 4 survey years. We recommend farmers in the study area prepare counter‐damage measures when the cumulative number of goose‐days per rice‐planted area approaches a threshold above which some geese are predicted to start foraging on wheat (e.g., 199.46 goose‐days/ha rice × 28.95 for 10% of geese foraging on wheat). Further, farmers should be aware that grazing on wheat is more likely to occur if wheat fields within 1,000–2,000 m have already been exploited during that particular season and should concentrate deterrence efforts to wheat fields that are far from roads and windbreaks. Systematic deployment of scaring devices over the entire habitat has a risk of accelerating the decline in effectiveness. Thus, we need methods to retard goose habituation to scaring devices, such as scaring with guns, providing alternative feeding sites, and preventing diet change by geese.
Waterfowl Nesting in Fall‐Seeded and Spring‐Seeded Cropland in Saskatchewan
Authors: DEVRIES JAMES H. , ARMSTRONG LLWELLYN M. , MACFARLANE ROBERT J. , MOATS LEE , THOROUGHGOOD PAUL T.
Published: October 2008

Abstract: Waterfowl nesting in annual croplands has remained a little‐known aspect of waterfowl nesting ecology because of the inability of many studies to systematically search this habitat through the nesting season. Where searches have been conducted, they are generally restricted to the period prior to seeding, and many nests found are destroyed by the seeding operation. Consequently, fall‐seeded crops have been promoted as an alternative cropping practice that could increase nest survival of waterfowl nesting in croplands. During 1996–1999, we conducted 3–4 complete nest searches on 4,274 ha of cropland, including spring‐seeded wheat and barley, winter wheat, and fall rye in southern Saskatchewan, Canada. Using suites of predictive models, we tested hypotheses regarding relative nest abundance and nest survival among crop types and tested the influence of several landscape‐scale covariates on these metrics. Apparent nest densities were higher in fall‐seeded crops (winter wheat: 0.39 nests/ha, fall rye: 0.25 nests/ha) than in spring‐seeded crops (0.03 nests/ha), and nest density in spring‐seeded croplands increased with percent cropland and percent wetland habitat in the surrounding landscape. Nest survival was higher in winter wheat (38%) than in either fall rye (18%) or spring‐seeded crops (12%), and nest survival in spring‐seeded crops increased with relative nest initiation date. Nest survival was unaffected by surrounding landscape characteristics but tended to be higher in years of average wetness. Based on our findings, winter wheat and fall rye have the potential to provide productive nesting habitat for ≥7 species of upland nesting ducks and fall‐seeded crops are a conservation tool well suited to highly cropped landscapes.
Grizzly Bear Density in Glacier National Park, Montana
Authors: KENDALL KATHERINE C. , STETZ JEFFREY B. , ROON DAVID A. , WAITS LISETTE P. , BOULANGER JOHN B. , PAETKAU DAVID
Published: October 2008

Abstract: We present the first rigorous estimate of grizzly bear (Ursus arctos) population density and distribution in and around Glacier National Park (GNP), Montana, USA. We used genetic analysis to identify individual bears from hair samples collected via 2 concurrent sampling methods: 1) systematically distributed, baited, barbed‐wire hair traps and 2) unbaited bear rub trees found along trails. We used Huggins closed mixture models in Program MARK to estimate total population size and developed a method to account for heterogeneity caused by unequal access to rub trees. We corrected our estimate for lack of geographic closure using a new method that utilizes information from radiocollared bears and the distribution of bears captured with DNA sampling. Adjusted for closure, the average number of grizzly bears in our study area was 240.7 (95% CI = 202–303) in 1998 and 240.6 (95% CI = 205–304) in 2000. Average grizzly bear density was 30 bears/1,000 km2, with 2.4 times more bears detected per hair trap inside than outside GNP. We provide baseline information important for managing one of the few remaining populations of grizzlies in the contiguous United States.
Assessing Estimators of Snow Leopard Abundance
Authors: MCCARTHY KYLE P. , FULLER TODD K. , MING MA , MCCARTHY THOMAS M. , WAITS LISETTE , JUMABAEV KUBANYCH
Published: October 2008

Abstract: The secretive nature of snow leopards (Uncia uncia) makes them difficult to monitor, yet conservation efforts require accurate and precise methods to estimate abundance. We assessed accuracy of Snow Leopard Information Management System (SLIMS) sign surveys by comparing them with 4 methods for estimating snow leopard abundance: predator:prey biomass ratios, capture‐recapture density estimation, photo‐capture rate, and individual identification through genetic analysis. We recorded snow leopard sign during standardized surveys in the SaryChat Zapovednik, the Jangart hunting reserve, and the Tomur Strictly Protected Area, in the Tien Shan Mountains of Kyrgyzstan and China. During June‐December 2005, adjusted sign averaged 46.3 (SaryChat), 94.6 (Jangart), and 150.8 (Tomur) occurrences/km. We used counts of ibex (Capra ibex) and argali (Ovis ammon) to estimate available prey biomass and subsequent potential snow leopard densities of 8.7 (SaryChat), 1.0 (Jangart), and 1.1 (Tomur) snow leopards/100 km2. Photo capture‐recapture density estimates were 0.15 (n = 1 identified individual/1 photo), 0.87 (n = 4/13), and 0.74 (n = 5/6) individuals/100 km2 in SaryChat, Jangart, and Tomur, respectively. Photo‐capture rates (photos/100 trap‐nights) were 0.09 (SaryChat), 0.93 (Jangart), and 2.37 (Tomur). Genetic analysis of snow leopard fecal samples provided minimum population sizes of 3 (SaryChat), 5 (Jangart), and 9 (Tomur) snow leopards. These results suggest SLIMS sign surveys may be affected by observer bias and environmental variance. However, when such bias and variation are accounted for, sign surveys indicate relative abundances similar to photo rates and genetic individual identification results. Density or abundance estimates based on capture‐recapture or ungulate biomass did not agree with other indices of abundance. Confidence in estimated densities, or even detection of significant changes in abundance of snow leopard, will require more effort and better documentation.
Statistical Confusion Among Graduate Students: Sickness or Symptom?
Authors: BOYLES JUSTIN G. , AUBREY DOUG P. , COOPER BRANDON S. , COX JONATHAN G. , COYLE DAVID R. , FISHER RYAN J. , HOFFMAN JUSTIN D. , STORM JONATHAN J.
Published: October 2008

Abstract: Statistics is one of the most important yet difficult subjects for many ecology and wildlife graduate students to learn. Insufficient knowledge about how to conduct quality science and the ongoing debate about the relative value of competing statistical ideologies contribute to uncertainties among graduate students regarding which statistical tests are most appropriate. Herein, we argue that increased education of the available statistical tests alone is unlikely to ameliorate the problem. Instead, we suggest that statistical uncertainties among graduate students are a secondary symptom of a larger problem. We believe the root cause lies in the lack of education on how to conduct science as an integrated process from hypothesis creation through statistical analysis. We argue that if students are taught to think about how each step of the process will affect all other steps, many statistical uncertainties will be avoided.
Instabilities and Transition to Chaos in Flows between Concentric Cylinders
Authors: Ait Aider Aomar
Published: October 2008

How does turbulence rise? For a long time, a century, the Taylor-Couette system was a paradigm for the researchers who tried to get answers to this question. Fascinating structures and patterns observed in the flow have attracted the interest of many researchers, both experimentalists and theorists. During the last century, many works were done on the closed Taylor-Couette systems. At the end of the seventies, after thousands of contributions, experiments performed in the Taylor-Couette system confirmed a theoretical analysis which concluded that a finite number of instabilities, two or three, are sufficient to lead to chaos or weak turbulence. Our own experiments were conducted at that time on a Taylor-Couette system with a moderate aspect ratio. They were analyzed from visual observation and fine local measurement with an electrochemical method. Scalar time series and data pointed out the frequencies characteristic of the flow. Many geometrical effects are considered by researchers. When the gap is horizontal and not completely filled, the flow obtained is called Taylor-Dean flow. We obtained similar flow in an azimuthally open Taylor-Couette system where a combination of the inner cylinder rotation and external fluid pumping, the Dean flow, produces the so called Taylor-Dean flow. Measurements and analysis were carried out by visualization and Laser Doppler Velocimetry. In addition to the experimental approach, we used Computational Fluid Dynamics analysis to complete the flow study. Numerical and experimental investigations reveal a class of instabilities of the Taylor-Dean flow not previously observed in the Taylor-Couette flow due to the cylinder rotation neither in the Dean flow due to the external pumping fluid.
Circulating Levels of Resistin and Risk of Type 2 Diabetes in Men and Women: Results From Two Prospective Cohorts
Authors: Chen Brian H. , Song Yiqing , Ding Eric L. , Roberts Christian K. , Manson JoAnn E. , Rifai Nader , Buring Julie E. , Gaziano J. Michael , Liu Simin
Published: October 2008

OBJECTIVE—The purpose of this study was to investigate the role of circulating resistin levels in the development of type 2 diabetes using two prospective cohorts of well-characterized men and women.

RESEARCH DESIGN AND METHODS—We conducted two prospective case-control studies nested in the Women's Health Study (WHS) and Physicians’ Health Study II (PHS II). In the WHS, during a median of 10-years of follow-up, 359 postmenopausal women, who were apparently healthy at baseline and later developed type 2 diabetes, were prospectively matched with 359 healthy control subjects. In the PHS II, with 8 years of total follow-up, 170 men, who were apparently healthy at baseline and later developed type 2 diabetes, were matched with 170 healthy control subjects. Control subjects were matched by age, race, and time of blood draw.

RESULTS—Resistin levels at baseline were significantly higher in women than in men (P = 0.003) and in case patients than in control subjects for both women (P < 0.001) and men (P = 0.07). After adjustment for matching factors, physical activity, alcohol intake, smoking, and family history of diabetes, the relative risk of type 2 diabetes comparing the highest to the lowest quartile of resistin in women was 2.22 ([95% CI 1.32–3.73]; Ptrend = 0.002). This association was attenuated after further adjustment for BMI (1.51 [0.86–2.65]; Ptrend = 0.20) or C-reactive protein (1.18 [0.68–2.07]; Ptrend = 0.60). A similar but weaker pattern was observed in men.

CONCLUSIONS—Elevated levels of circulating resistin were significantly related to increased risk of type 2 diabetes, which appears to be partially accounted for by adiposity and the inflammatory process.
A cyclic universe with colour fields
Authors: Yershov Vladimir
Published: October 2008

The topology of the universe is discussed in relation to the singularity problem. We explore the possibility that the initial state of the universe might have had a structure with 3-Klein bottle topology, which would lead to a model of a nonsingular oscillating (cyclic) universe with a well-defined boundary condition. The same topology is assumed to be intrinsic to the nature of the hypothetical primitive constituents of matter (usually called preons) giving rise to the observed variety of elementary particles. Some phenomenological implications of this approach are also discussed.
Microstructure and thermal properties of quasi-equal rare earth substitution Y0.5Gd0.5Ba2Cu3O6.94 superconductor
Authors: Terzieva Stanimira , Stoyanova-Ivanova Angelina , Shivachev Boris , Terzijska Bonka , Zaleski Andrzej , Misiorek Halina , Mikli Valdek
Published: October 2008

Sintering effects in YBa2Cu3Oz samples with quasi-equal rare earth substitution have been investigated. It has been shown that the Y-123 type compound can be formed when gadolinium is partially substituted (in this case 50% atomic substitution) for yttrium. The superconducting compound was obtained by the optimized ceramic method, including solid-state reaction, melting and sintering, controlled by X-ray diffraction. The microstructure was investigated by SEM and energy dispersive X-ray analyses. An AC susceptibility measurement has shown that T
c =93 K. Temperature-dependece of the thermal conductivity (4.5–300 K) of the polycrystalline Y0.5Gd0.5Ba2Cu3O6.94 sample was also measured.
The use of reverse-flow dorsal metacarpal artery flaps after postburn metacarpophalangeal joint flexion contracture release
Authors: Duman Haluk , Uygur Fatih , Evinç Rahmi
Published: October 2008

When thermal injuries of the hand are managed inappropriately, complex hand contractures are inevitable. Patients with hand contractures may have many difficulties in their daily life because of this deformity. These patients are challenging to reconstructive surgeons. In this study we evaluated reverse-flow dorsal metacarpal artery flaps for the defects occurred after metacarpophalangeal joint contracture release of different fingers. Nineteen patients with defects on the volar surface of metacarpophalangeal joint were reconstructed by the reverse-flow dorsal metacarpal artery flaps. All operations were successful and flap losses were not seen. The DMCA flaps provide one stage coverage and permit primary closure of the recipient site. The aesthetic and functional results are satisfactory without sacrificing main arteries. The only drawback is the residual scar on the dorsum of the hand, which can be treated by conservative means and may improve over time.
Paraurethral cyst: a case report
Authors: Ceyhan Meltem , Nural Mehmet , Oztas Tülin , Bayrak İlkay , Rizalar Riza
Published: October 2008

Paraurethral or Skene’s duct cyst is a rare cause of masses located in the inter-labial genitor-urinary region and their etiology is not fully known. These congenital cysts may be diagnosed easily by inspection in the initial physical examination of the new-borne. Radiological evaluation is helpful for differential diagnosis and in determining the proximal extension of the cystic pathology. Treatment alternatives are needle aspiration and non-surgical follow-ups leading to a spontaneous regression and surgery. In this report the radiological findings of a female newborn diagnosed with paraurethral cyst in US and MR examinations have been discussed.
New Prayers, Here and Now: Reconnecting to Israel Through Engaging in Prayer, Poetry, and Song
Authors: Newberg Adina B.
Published: October 2008

Israelis who have until now viewed themselves as "secular" in the rigid Israeli dichotomy between "religious" and "secular" are finding new ways of creating communities of meaning that connect to Jewish sources and yet stay aligned to values of pluralism and humanism.

These communities that do not follow the letter of the halakhah are developing in highly "secular" environments such as Tel Aviv and Nahalal and create Shabbat and holiday services combining live music, traditional prayers, and newly created prayers. By doing this, they come nearer to finding a closer echo and a truer mirror to their concerns and spiritual searches while, at the same time, finding spiritual expressions to their deep longing for connection to Judaism. Beyond the services and the communities that are forged, a new identity that bridges aspects of secularism, humanism, and spirituality is being created.

The article analyzes the reasons for this relatively new phenomenon in the context of Israeli religious and political life, and the existential crisis that has evolved as a result. The article also describes in detail two such communities as examples of this development.
One Meeting—Many Descriptions: The Resolution on the Establishment of the State of Israel
Authors: Feldestein Ariel L.
Published: October 2008

This year, Israel marks the sixtieth anniversary of the establishment of the state. It is an opportune time to study anew the discussions in the People's Administration, which was founded on the eve of the declaration of statehood. In this article, I will examine the course of the discussions and the voting with regard to the declaration, as reflected in the primary sources, in the oral interviews with members of the People's Administration, and in the historiographic descriptions.
Simulation de la structure optimale des hêtraies de protection contre les chutes de pierres | Simulation of the optimal structure of beech forests protecting against rockfall
Authors: Vienne Françoise , Bugmann Harald , Zingg Andreas , Frehner Monika
Published: October 2008

Adequate management practices to attain the profiles specified in the Swiss guidelines for the management of mountain protection forests are not always unequivocally clear. This applies among others for beech forests that have a protective function against rockfall. We defined two management scenarios, one of which aims at harvesting trees starting with a minimum diameter at breast height of 40 cm, whereas the other one is focused on the creation of small gaps (area of 500 m2) over a maximum of 10% of the total stand area. These scenarios along with a control scenario characterized by no management were studied using the forest growth model BWINPro. In the control scenario, number of trees, basal area and standing volume were highest. The developments simulated under the two management scenarios were similar, when in scenario thinning harvesting levels corresponded to the growth over a 10-year period. In the other cases, number of trees, basal area and standing volume are lower under scenario gap because harvesting interventions occur more regularly. If the rocks have a volume exceeding 0.2 m3, the requirements of the profiles are attained more quickly under scenario gap, because in scenario thinning the larger trees are preferentially harvested. Because tree regeneration was not simulated, it is difficult to realistically predict the development of the number of trees. However, management interventions are needed in such forests, particularly if the profile for rocks with a volume below 0.2 m3 is to be attained and maintained.
Characterizing Cavities in Model Inclusion Fullerenes: A Comparative Study
Authors: Torrens Francisco
Published: October 2008

The fullerene-82 cavity is selected as a model system in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecular surface, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and cubic lattice approach to the molecular volume. Accurate measures of the molecular volume and surface area have been performed with the pseudorandom Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the rest of the methods. The SURMO2 method does not recognize the cavity and may not be convenient for intercalation compounds. The programs that detect the cavities never exceed 1% deviation relative to the reference value for molecular volume and 5% for surface area. The GEPOL algorithm, alone or combined with TOPO, shows results in good agreement with those of the UMCVS reference. The uniform random number generator provides the fastest convergence for UMCVS and a correct estimate of the standard deviations. The effect of the internal cavity on the solvent-accessible surfaces has been calculated. Fullerene-82 is compared with fullerene-60 and -70.
Variational Perturbation Theory of the Confined Hydrogen Atom
Authors: Montgomery H. E.
Published: October 2008

Variational perturbation theory was used to solve the Schrödinger equation for a hydrogen atom confined at the center of an impenetrable cavity. Ground state and excited state energies and expectation values calculated from the perturbation wavefunction are comparable in accuracy to results from direct numerical solution.
Is Electronic Publishing Being Used in the Best Interests of Science? The Scientist’s View
Authors: Berry R.  Stephen
Published: October 2008

The term "the best interests of science" must be interpreted from the viewpoints both of the scientists inside the enterprise and of the supporters and "users" affected by society's using the results of scientific research. This presentation will try to interpret the material presented throughout the Conference [1] in terms of both these viewpoints, but all within the context of this presenter's perspective, as a scientist, regarding "Why should we have science?" This presentation will be an overview and summary of many ideas that emerged in discussions in the Conference, with no attempt to attribute those ideas to individuals because so many of them were said by several participants, here and elsewhere. Furthermore, the perspective here is certainly that of the scientist, not of the publisher.
New Strategies for the Improvement of Automobile Catalysts
Authors: Fernández-García M. , Martínez-Arias A. , Iglesias-Juez A. , Hungría A. B. , Anderson J. A. , Conesa J. C. , Soria J.
Published: October 2008

This paper provides a review of recently obtained spectroscopic results, ab-initio calculations and catalytic activity tests from the authors´ laboratory of factors affecting the performance of materials used as automobile catalysts. Issues addressed include the preparation of (Ce,Zr)Ox/Al2O3 (CZA) mixed oxide supports and the use of new active metals, such as Pd and Cu, for three-way catalysts (TWCs); the performance of non-noble transition metals, such as Co or Ag, for pollution control under lean conditions; and the use of Pt/BaOx/Al2O3 (PtBa) for engine exhaust gas treatment under oscillating lean-stoichiometric conditions.
A First Principles Density Functional Study of Au Deposition on TiN (001) Surface
Authors: Hernández Norge  Cruz , Sanz Javier  Fdez.
Published: October 2008

The structure and local electron properties of Au atoms deposited on the TiN (001) surface has been theoretically analyzed using a periodic slab model and density functional based calculations. The surface is described by means of a 2x2 cell five layers thick, on which gold atoms are added. Deposition of single atoms on the surface, (θ = 0.25 ML), shows that the preferred site is on-top of Ti atoms, with a metal-surface distance of 2.49 Å. The computed adsorption energy for this site is -1.92 eV, only slightly lower than that lying between two Ti surface atoms (-1.90 eV). The on-top nitrogen sites are less favorable by about 0.4 eV. The calculations were carried out using the Perdew-Wang 91 exchange correlation functional and ultra soft pseudopotentials, with electronic states represented by a plane-wave expansion.
A First-Principles Study of the Ag/a-Al2O3(0001) Interface
Authors: Zhukovskii Yu. F. , Kotomin E. A. , Herschend B. , Hermansson K. , Jacobs P. W.M.
Published: October 2008

Ab initio simulations of the Ag/a-Al2O3(0001) interface have been performed for periodic slab models. We have considered Al- and O-terminated corundum surfaces, low and high substrate coverages by silver, as well as the two preferred Ag adsorption sites. The two different terminations give rise to qualitatively different results: silver physisorption on the Al-terminated substrate and chemisorption on O-terminated one. The latter could be treated as a possible model for the defective Al-terminated substrate, where the outermost aluminium ions are removed (completely or partly). This makes O-terminated surface highly reactive towards a deposited metal, in order to restore initial corundum stoichiometry.
R. Stephen Berry
Authors: Proykova Ana
Published: October 2008

A James Franck Distinguished Service Professor of Chemistry at the University of Chicago, R. Stephen Berry has worked on a variety of subjects ranging from strictly scientific matters to the analysis of energy use and resource policy.[...]
Real-space renormalization group study of the Hubbard model on a non-bipartite lattice
Authors: Wang J. X. , Kais Sabre , Levine R. D.
Published: October 2008

We present the real-space block renormalization group equations for fermion systems described by a Hubbard Hamiltonian on a triangular lattice with hexagonal blocks. The conditions that keep the equations from proliferation of the couplings are derived. Computational results are presented including the occurrence of a first-order metal-insulator transition at the critical value of U/t ≈ 12.5.
Global Optimization by Adiabatic Switching
Authors: Hunjan Jagtar S. , Ramaswamy R.
Published: October 2008

We apply a recently introduced method for global optimization to determine the ground state energy and configuration for model metallic clusters. The global minimum for a given N–atom cluster is found by following the damped dynamics of the N particle system on an evolving potential energy surface. In this application, the time dependent interatomic potential interpolates adiabatically between the Lennard–Jones (LJ) and the Sutton–Chen (SC) forms. Starting with an ensemble of initial conditions corresponding to the ground state configuration of the Lennard–Jones cluster, the system asymptotically reaches the ground state of the Sutton–Chen cluster. We describe the method and present results for specific cluster size N = 15, when the ground state symmetry of LJN and SCN differ.
Theoretical Calculation of Absolute Radii of Atoms and Ions. Part 1. The Atomic Radii
Authors: Ghosh Dulal C. , Biswas Raka
Published: October 2008

A set of theoretical atomic radii corresponding to the principal maximum in the radial distribution function, 4πr2R2 for the outermost orbital has been calculated for the ground state of 103 elements of the periodic table using Slater orbitals. The set of theoretical radii are found to reproduce the periodic law and the Lother Meyer’s atomic volume curve and reproduce the expected vertical and horizontal trend of variation in atomic size in the periodic table. The d-block and f-block contractions are distinct in the calculated sizes. The computed sizes qualitatively correlate with the absolute size dependent properties like ionization potentials and electronegativity of elements. The radii are used to calculate a number of size dependent periodic physical properties of isolated atoms viz., the diamagnetic part of the atomic susceptibility, atomic polarizability and the chemical hardness. The calculated global hardness and atomic polarizability of a number of atoms are found to be close to the available experimental values and the profiles of the physical properties computed in terms of the theoretical atomic radii exhibit their inherent periodicity. A simple method of computing the absolute size of atoms has been explored and a large body of known material has been brought together to reveal how many different properties correlate with atomic size.
Anisotropy effects in H++H2 collisions
Authors: Errea L. , Macías A. , Méndez L. , Rabadán I. , Riera A.
Published: October 2008

The effect of the anisotropy of the interaction potential on ion-diatom non-adiabatic collisions is analized by considering the influence of the anisotropy on orientation averaged total cross sections for charge transfer in H++H2(X1Σ+g ) collisions. We discuss the possibility of employing simpli ed methods such as an isotropic approximation, where only the electronic energies and interactions of a single orientation are necessary. The use of several isotropic calculations to evaluate the orientation averaged cross section is analized.
Studies of Electron Capture by Multiply Charged Ions from Molecules using Translational Energy Spectroscopy
Authors: Kearns D. M. , McCullough R. W. , Gilbody H. B.
Published: October 2008

The development of experimental ion-trap techniques provides the opportunity to compare directly theoretical rate coefficients to experimental data in the low-temperature regime. In the present work, we consider the ion-atom collisional systems, N2+, O2+, Si3+ and Si4+ on a He target, in order to examine the present status of the agreement between theory and experiment.
The Law of Mass Action
Authors: Lin Shu-Kun
Published: October 2008

During the weekend I quickly browsed through this book [2] with great interest and recommend all chemists, whether experimental chemists or theoretical chemists, to read it.[...]
Special Issue on Application of Density Functional Theory in Chemical Reactions
Authors: Chatterjee Abhijit
Published: October 2008

Rapid advances are taking place in the application of density functional theory (DFT) to describe complex chemical reactions.[...]
Applications of the Information Theory to Problems of Molecular Electronic Structure and Chemical Reactivity
Authors: Nalewajski Roman F.
Published: October 2008

Recent studies on applications of the information theoretic concepts to molecular systems are reviewed. This survey covers the information theory basis of the Hirshfeld partitioning of molecular electron densities, its generalization to many electron probabilities, the local information distance analysis of molecular charge distributions, the charge transfer descriptors of the donor-acceptor reactive systems, the elements of a “thermodynamic” description of molecular charge displacements, both “vertical” (between molecular fragments for the fixed overall density) and “horizontal” (involving different molecular densities), with the entropic representation description provided by the information theory. The average uncertainty measures of bond multiplicities in molecular “communication” systems are also briefly summarized. After an overview of alternative indicators of the information distance (entropy deficiency, missing information) between probability distributions the properties of the “stockholder” densities, which minimize the entropy deficiency relative to the promolecule reference, are summarized. In particular, the surprisal analysis of molecular densities is advocated as an attractive information-theoretic tool in the electronic structure theory, supplementary to the familiar density difference diagrams. The subsystem information density equalization rules satisfied by the Hirshfeld molecular fragments are emphasized: the local values of alternative information distance densities of subsystems are equal to the corresponding global value, characterizing the molecule as a whole. These local measures of the information content are semi-quantitatively related to the molecular density difference function. In the density functional theory the effective external potentials of molecular fragments are defined, for which the subsystem densities are the ground-state densities. The nature of the energetic and “entropic” equilibrium conditions is reexamined and the entropy representation forces driving the charge transfer in molecular systems are introduced. The latter combine the familiar Fukui functions of subsystems with the information densities, the entropy representation “intensive” conjugates of the subsystem electron densities, and are shown to exactly vanish for the “stockholder” charge distribution. The proportionality relations between charge response characteristics of reactants, e.g., the Fukui functions, are derived. They are shown to follow from the minimum entropy deficiency principles formulated in terms of both the subsystems electron densities and Fukui functions, respectively.
Density Functional Theory and Materials Modeling at Atomistic Length Scales
Authors: Ghosh Swapan K.
Published: October 2008

We discuss the basic concepts of density functional theory (DFT) as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.
Chemical Reactivity as Described by Quantum Chemical Methods
Authors: Geerlings P. , De Proft F.
Published: October 2008

Density Functional Theory is situated within the evolution of Quantum Chemistry as a facilitator of computations and a provider of new, chemical insights. The importance of the latter branch of DFT, conceptual DFT is highlighted following Parr's dictum "to calculate a molecule is not to understand it". An overview is given of the most important reactivity descriptors and the principles they are couched in. Examples are given on the evolution of the structure-property-wave function triangle which can be considered as the central paradigm of molecular quantum chemistry to (for many purposes) a structure-property-density triangle. Both kinetic as well as thermodynamic aspects can be included when further linking reactivity to the property vertex. In the field of organic chemistry, the ab initio calculation of functional group properties and their use in studies on acidity and basicity is discussed together with the use of DFT descriptors to study the kinetics of SN2 reactions and the regioselectivity in Diels Alder reactions. Similarity in reactivity is illustrated via a study on peptide isosteres. In the field of inorganic chemistry non empirical studies of adsorption of small molecules in zeolite cages are discussed providing Henry constants and separation constants, the latter in remarkable good agreement with experiments. Possible refinements in a conceptual DFT context are presented. Finally an example from biochemistry is discussed : the influence of point mutations on the catalytic activity of subtilisin.
The O-H Bond Dissociation Energies of Substituted Phenols and Proton Affinities of Substituted Phenoxide Ions: A DFT Study
Authors: Chandra Asit , Uchimaru Tadafumi
Published: October 2008

The accurate O-H bond dissociation enthalpies for a series of meta and para substituted phenols (X-C6H4-OH, X=H, F, Cl, CH3, OCH3, OH, NH2, CF3, CN, and NO2) have been calculated by using the (RO)B3LYP procedure with 6-311G(d,p) and 6-311++G(2df,2p) basis sets. The proton affinities of the corresponding phenoxide ions (XC6H4-O-) have also been computed at the same level of theory. The effect of change of substituent position on the energetics of substituted phenols has been analyzed. The correlations of Hammett’s substituent constants with the bond dissociation enthalpies of the O-H bonds of phenols and proton affinities of phenoxide ions have been explored.
New Transcorrelated Method Improving the Feasibility of Explicitly Correlated Calculations
Authors: Ten-no Seiichiro , Hino Osamu
Published: October 2008

We recently developed an explicitly correlated method using the transcorrelated Hamiltonian, which is preliminarily parameterized in such a way that the Coulomb repulsion is compensated at short inter-electronic distances. The extra part of the effective Hamiltonian features short-ranged, size-consistent, and state-universal. The localized and frozen nature of the correlation factor makes the enormous three-body interaction less important and enables us to bypass the complex nonlinear optimization. We review the basic strategy of the method mainly focusing on the applications to single-reference many electron theories using modified Møller-Plesset partitioning and biorthogonal orbitals. Benchmark calculations are performed for 10-electron systems with a series of basis sets.