bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Counseling Supervisor Competencies: Results of a Delphi Study
Authors: Eubanks Higgins Sonja , Veach Patricia McCarthy , MacFarlane Ian M. , Borders L. DiAnne , LeRoy Bonnie , Callanan Nancy 
Published: June 2012

AbstractClinical supervision is a critical component of genetic counseling student preparation, yet empirically‐determined competencies for genetic counseling supervisors are lacking. In this study a modified, two‐round Delphi method was used to gain consensus about important genetic counseling supervisor knowledge, characteristics, and skills. Program directors and assistant directors of American Board of Genetic Counseling accredited genetic counseling programs in North America (N = 33) were invited to participate and to recruit three experienced supervisors. Seventy‐four individuals completed Round 1 and, of these, 61 completed Round 2. Approximately two‐thirds were clinical supervisors from prenatal, pediatrics, cancer, and adult clinics; one‐third were program directors. Participants rated the importance for genetic counseling supervisors of 158 items derived from supervision literature in allied health professions. They rated 142 items (89.9 %) as highly important. Content analysis of these items yielded six supervisor competency domains: Personal traits and characteristics; relationship building and maintenance; student evaluation; student centered supervision; guidance and monitoring of patient care; and ethical and legal aspects of supervision. The results provide a basis for training genetic counseling supervisors and for further research to refine and validate supervisor competencies.
True Markowitz or assumptions we break and why it matters
Authors: Wilford D. Sykes 
Published: June 2012

AbstractMarkowitz (1952, 1959) underlies modern corporate finance literature, from modern portfolio theory, option theory, to risk management (especially value at risk type methodologies). From it, Diversify has entered all languages, such is its power. Terms such as “the only free lunch” have become a way to give praise to Markowitz work. And, just as with all fundamental breakthroughs in the literature it has been extended many directions, sometimes not necessarily to the benefit of the original work, which often gets blamed when one rendition or another breaks down. With almost every MBA graduated believing they know what Markowitz optimization or portfolio theory means, it behooves us to step back and look at some of the basics, the assumptions that are made, the costs of breaking assumptions, and the potential disasters that can occur when those basics behind all of the theories dependent upon Markowitz' original work are ignored.This paper lays out many of the basic underlying assumptions behind creation of Markowitz type portfolios, why they matter, and where those assumptions are ignored and/or broken. Breaking model assumptions is common in actual application of theory. Not understanding the implications of broken assumptions is almost a guarantee of failure for a money manager; it is just a matter of time. As one often hears, “Wall Street (or the City if in Europe) is littered with great ideas that do not work in practice.” Some people throw Markowitz and portfolio optimization into that litter bin. We discuss several basic assumptions of modern portfolio theory, when and why they are commonly broken by the best of us in academia and in practice, and discuss the implications for breaking them under trying circumstances.
Straightforward reconstruction of 3D surfaces and topography with a camera: Accuracy and geoscience application
Authors: James M. R. , Robson S. 
Published: June 2012

Topographic measurements for detailed studies of processes such as erosion or mass movement are usually acquired by expensive laser scanners or rigorous photogrammetry. Here, we test and use an alternative technique based on freely available computer vision software which allows general geoscientists to easily create accurate 3D models from field photographs taken with a consumer‐grade camera. The approach integrates structure‐from‐motion (SfM) and multiview‐stereo (MVS) algorithms and, in contrast to traditional photogrammetry techniques, it requires little expertise and few control measurements, and processing is automated. To assess the precision of the results, we compare SfM‐MVS models spanning spatial scales of centimeters (a hand sample) to kilometers (the summit craters of Piton de la Fournaise volcano) with data acquired from laser scanning and formal close‐range photogrammetry. The relative precision ratio achieved by SfM‐MVS (measurement precision: observation distance) is limited by the straightforward camera calibration model used in the software, but generally exceeds 1:1000 (i.e., centimeter‐level precision over measurement distances of 10 s of meters). We apply SfM‐MVS at an intermediate scale, to determine erosion rates along a ∼50‐m‐long coastal cliff. Seven surveys carried out over a year indicate an average retreat rate of 0.70 ± 0.05 m a−1. Sequential erosion maps (at ∼0.05 m grid resolution) highlight the spatiotemporal variability in the retreat, with semivariogram analysis indicating a correlation between volume loss and length scale. Compared with a laser scanner survey of the same site, SfM‐MVS produced comparable data and reduced data collection time by ∼80%.
Parameterized lifetime of radiation belt electrons interacting with lower‐band and upper‐band oblique chorus waves
Authors: Gu Xudong , Shprits Yuri Y. , Ni Binbin 
Published: June 2012

In order to evaluate the electron lifetimes from quasi‐linear bounce‐averaged diffusion coefficients, a large amount of CPU time is required to compute scattering rates. To reduce computation time, we assume that the electron loss rates are a function of L shell and electron energy, allowing us to derive the parameterization of electron lifetime using a linear regression technique. We also present the parameterizations of lifetimes as a function of electron energy and ratios of plasma frequency to electron gyrofrequency at a fixed L shell. By considering the net loss rates due to lower‐band (0.05–0.5 |Ωce|) and upper‐band (0.5–0.7 |Ωce|) chorus waves propagating obliquely with respect to the ambient magnetic field, the parameterizations of electron lifetime for energies between 1 keV and 2 MeV are investigated in the outer radiation belt. The parameterized lifetimes indicate a strong functional dependence on electron energy, L shell, and the level of geomagnetic activity (Kp index), and are also dependent on the ratios of plasma frequency to electron gyrofrequency. During the storm time, the lifetimes for higher energy (>100 keV) electrons range from hours to days in the heart of the radiation belts. In contrast, the lifetimes for lower energy (<100 keV) electrons are mainly in the range from minutes to hours. Such parameterization efforts of radiation belt electron lifetimes are very significant for multi‐dimensional simulations of the dynamics of the radiation belt and ring current electrons.
Pre‐Columbian deforestation as an amplifier of drought in Mesoamerica
Authors: Cook B. I. , Anchukaitis K. J. , Kaplan J. O. , Puma M. J. , Kelley M. , Gueyffier D. 
Published: June 2012

Droughts in pre‐Columbian Mesoamerica caused significant societal disruptions during the Late Classic and Post‐Classic Periods. While the primary causes of these droughts are still debated, it has been speculated that they may be linked to extensive deforestation associated with high population densities during these intervals. Here we show that pre‐Columbian deforestation would have biased the climate in Mesoamerica towards a drier mean state, amplifying drought in the region. In climate model simulations using a pre‐Columbian land cover reconstruction, annual precipitation decreases by 5%–15% throughout southern Mexico and the Yucatán compared to simulations using either natural forest cover or forest regrowth associated with population declines after 1500 C.E. These changes are driven primarily by large reductions (10%–20%) in precipitation during the late summer wet season (August–September). When compared to precipitation changes estimated to have occurred during the Maya collapse, our results suggest that deforestation could account for up to sixty percent of the mean drying during this interval. Many regions previously deforested in the pre‐Columbian era are now under dense forest cover, indicating potential future climate impacts should tropical deforestation of these areas accelerate.
Crystals stirred up: 2. Numerical insights into the formation of the earliest crust on the Moon
Authors: Suckale Jenny , Elkins‐Tanton Linda T. , Sethian James A. 
Published: June 2012

This is the second paper in a two‐part series examining the fluid dynamics of crystal settling and flotation in the lunar magma ocean. In the first paper, we develop a direct numerical method for resolving the hydrodynamic interactions between crystals and their feedback on the flow field in magmatic liquid. In this paper, we use this computational technique to test the leading model for the formation of the earliest crust on the Moon. The anorthositic lithology of the lunar crust is thought to have been formed by the flotation of buoyant plagioclase crystals at a time when the lunar mantle was still wholly or largely molten. This model is appealing from an observational point of view, but its fluid dynamical validity is not obvious, because (1) plagioclase probably started crystallizing very late (i.e., when the magma ocean was already 80% solidified) and (2) a significant portion of the shallow lunar crust consists of almost pure plagioclase (>90 vol. %), requiring very efficient plagioclase segregation. The goal of this study is to better understand the fluid dynamical conditions that hinder or facilitate crystal settling or flotation. Our approach complements earlier studies by explicitly linking the petrological and fluid dynamical evolution and by focusing on the effect of increasing crystal fraction. We find that crystal settling was probably possible throughout the entire solidification history of the lunar magma ocean as long as crystal sizes were sufficiently large (r > 1 mm) and crystal fraction sufficiently low (ϕ < 13%).
Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples
Authors: Lange Oliver F. , Rossi Paolo , Sgourakis Nikolaos G. , Song Yifan , Lee Hsiau-Wei , Aramini James M. , Ertekin Asli , Xiao Rong , Acton Thomas B. , Montelione Gaetano T. , Baker David 
Published: June 2012

We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the “best effort” structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.
Rapid hybridization of nucleic acids using isotachophoresis
Authors: Bercovici Moran , Han Crystal M. , Liao Joseph C. , Santiago Juan G. 
Published: June 2012

We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.
Evidence of Recent Climate Change within the Historic Range of Rio Grande Cutthroat Trout: Implications for Management and Future Persistence
Authors: Zeigler Matthew P. , Todd Andrew S. , Caldwell Colleen A. 
Published: June 2012

AbstractEvidence of anthropogenically influenced climate change has motivated natural resource managers to incorporate adaptive measures to minimize risks to sensitive and threatened species. Detecting trends in climate variables (i.e., air temperature and hydrology) can serve as a valuable management tool for protecting vulnerable species by increasing our understanding of localized conditions and trends. The Rio Grande cutthroat trout Oncorhynchus clarkii virginalis has suffered a severe decline in its historical distribution, with the majority of current populations persisting in isolated headwater streams. To evaluate recent climate change within the subspecies’ historical range, we examined trends in average air temperatures, biologically important hydrological variables (timing of snowmelt and seasonal flows), and the April 1 snow water equivalent over the last 45 years (1963–2007). While rates of change in all three metrics were variable across sites, rangewide patterns were evident. Across the subspecies’ historical range, average annual air temperatures increased (0.29°C per decade) and the timing of snowmelt shifted 10.6 d earlier in the year (2.3 d/decade). Flows increased during biologically important periods, including winter (January 1–March 31; 6.6% increase per decade), prespawning (April 1–May 14; 6.9% increase per decade), and spawning (May 15–June 15; 4.2% increase per decade) and decreased in summer (June 16–September 15; 1.9% decrease per decade). Evidence of decreasing April 1 snow water equivalent (5.3% per decade) was also observed. While the impacts of these changes at the population level are equivocal, it is likely that negative effects would influence the subspecies by altering its distribution, decreasing available habitat, and altering the timing of important life history components. Continued monitoring and proactive management will be required to increase the resiliency of remaining populations to ensure long‐term persistence and protection in a changing climate.
Digital repositories ten years on: what do scientific researchers think of them and how do they use them?
Authors: NICHOLAS David , ROWLANDS Ian , WATKINSON Anthony , BROWN David , JAMALI Hamid R. 
Published: June 2012

ABSTRACTDigital repositories have been with us for more than a decade, and despite the considerable media and conference attention they engender, we know very little about their use by academics. This paper sets out to address this by reporting on how well they are used, what they are used for, what researchers' think of them, and where they thought they were going. Nearly 1,700 scientific researchers, mostly physical scientists, responded to an international survey of digital repositories, making it the largest survey of its kind. High deposit rates were found and mandates appear to be working, especially with younger researchers. Repositories have made significant inroads in terms of impact and use despite, in the case of institutional repositories, the very limited resources deployed. Subject repositories, like arXiv and PubMed Central, have certainly come of age but institutional repositories probably have not come of age yet although there are drivers in place which, in theory anyway, are moving them towards early adulthood.
Selling to the BRIC: the background to the scholarly publishing market in India
Authors: MALIK Rakesh 
Published: June 2012

ABSTRACTThis article provides an overview of the Indian scholarly publishing market in terms of the demographics, market verticals, research institutions, sources and patterns of funding, and the burgeoning potential of the globalised Indian economy. It explores the feasibility for entry of international publishers and tried and tested business models. The analysis covers the nuances of the growth drivers and inhibitors, the current success and status of existing players, and the key challenges.
The importance of whether atrial fibrillation or heart failure develops first
Authors: Smit Marcelle D. , Moes Marjolein L. , Maass Alexander H. , Achekar Ismaël D. , Van Geel Peter P. , Hillege Hans L. , van Veldhuisen Dirk J. , Van Gelder Isabelle C. 
Published: June 2012

AimsAtrial fibrillation (AF) and heart failure often co‐exist. It is unknown whether the sequence in which AF and heart failure develop is of significance regarding prognosis. We assessed the prognosis of AF patients hospitalized for heart failure based on the timing of AF and heart failure development.Methods and resultsConsecutive AF patients hospitalized for heart failure were included. Patients who had developed AF before or consecutively with heart failure (‘AF first’) were compared with patients who had developed heart failure before AF (‘heart failure first’). The primary endpoint was a composite of cardiovascular hospitalization or all‐cause mortality. The majority of patients hospitalized for AF and heart failure consisted of patients who had developed AF first (137 of 182 patients, 75%, vs. 45 of 182 patients, 25%). The two groups were similar regarding age and gender, but patients with AF first less often had coronary artery disease and had higher ejection fractions than patients with heart failure first (39 ±14% vs. 32 ±13%, P =0.004). During 16 ±11 months follow‐up, the primary composite endpoint occurred less often in patients with AF first than in patients with heart failure first (49.6% vs. 77.7% of patients, P =0.001). Development of AF first remained beneficial regarding the primary endpoint on multivariable analysis (adjusted hazard ratio 0.50, 95% confidence interval 0.29–0.86, P =0.01).ConclusionThe majority of patients hospitalized for AF and heart failure consisted of patients who had developed AF first. Prognosis in these patients was relatively benign as compared with those who had developed heart failure first.
A review of the Sea of Okhotsk ecosystem response to the climate with special emphasis on fish populations
Authors: Kim Sen Tok 
Published: June 2012

Abstract
Kim, S. T. 2012. A review of the Sea of Okhotsk ecosystem response to the climate with special emphasis on fish populations. – ICES Journal of Marine Science, 69: . This article provides a brief review of climatic, oceanographic, and biological changes in the Sea of Okhotsk in recent decades. The Sea of Okhotsk is distinguished by its high biological productivity and its significant impact on the Pacific Ocean through water exchanges. Long-term temperature data have shown periodic cooling and warming of the Sea that in turn have resulted in changes to its biological communities. In the 1980s, a generally warm period, the Sea of Okhotsk had abundant fish, primarily large stocks of gadoids, especially walleye pollock. The second half of the 1990s was a transitional period when the marine ecosystem was being restructured. In particular, by the mid-1990s, the total biomass of fish in the Sea of Okhotsk had decreased significantly. In the early 2000s, the situation reached a critical level, but by the end of that decade, there was a renewed warming and an increase in the abundance of walleye pollock.
First Report of Root-Knot Nematode Meloidogyne arenaria on Atractylodis macrocephalae in China
Authors: Wang X. Z. , Wang L. F. , Piao C. G. , Guo M. W. , Li Y. 
Published: June 2012

Atractylodis macrocephalae is an important Chinese herbal medicine plant and its rhizome is of high medicinal value. In recent years, a severe decline in yield has been observed in Bozhou City (China's largest A. macrocephalae producing area), Anhui Province, China. A survey for plant-parasitic nematodes was conducted in this area from June to September 2011. Stunted plants displayed chlorotic or necrotic lower leaves near the ground part by the growth reduction; examination of the roots of stunted plants revealed the presence of galls typical of infestation by root knot nematode. Root nodules were found on the tap and lateral roots caused the fleshy tap root deformity. The incidence of diseased plants was estimated to be 45%, and yield loss was quantified as 43.5%. Nematodes were extracted from the root samples as previously described (4) and identified by morphology, enzyme analysis, and molecular characterization. Morphology of the female perineal patterns and measurements of the second-stage juveniles (J2s) matched those of the original description of Meloidogyne arenaria. Enzyme analysis of the esterase (Est) phenotype was also typical of the AII phenotype in M. arenaria (2). DNA was extracted according to a modified protocol (1), and the rDNA-internal transcribed spacer (ITS1_5.8S_ITS2) region was amplified with universal primers V5367 (5′-TTGATTACGTCCCTGCCCTTT-3′) and 26S (5′-TTTCACTCGCCGTTACTAAGG-3′). PCR yielded a fragment of 764 bp and the purified product was sequenced by Sanger's dideoxy chain termination method (ABI3730). Sequences were identical to that of M. arenaria in GenBank (Accession No. AF387092) (3). Amplification of the D2/D3 fragments of the 28S RNA with universal primers D2A (5′-ACAAGTACCGTGAGGGAAAGTTG-3′) and D3B (5′-TCGGAAGGAACCAGCTACTA-3′) yielded a PCR fragment of 758 bp. These sequences were also identical to that of M. arenaria in GenBank (Accession No. AF435803). For further confirmation, amplification of the IGS region with universal primers 5S (5′-TTAACTTGCCAGATCGGACG-3′) and 18S (5′-TCTAATGAGGGAACCAGCTACTA-3′) yielded a PCR fragment of 713 bp. These sequences were 99.64% homologous to that of M. arenaria (GenBank Accession No. MAU42342). To our knowledge, this is the first report of M. arenaria species on A. macrocephalae in China. The fleshy tap root of A. macrocephalae is the main edible part of the plant, and the damage caused by root knot nematode will potentially reduce the yield and quality of this herb. References: (1) J. L. Cenis et al. Phytopathology 83:76, 1993. (2) P. R. Esbenshade and A. C. Triantaphyllou. J. Nematol. 17:6, 1985. (3) T. C. Vrain et al. Appl Nematol. 15:563, 1992. (4) L. F. Wang et al. Forest Res. 14:484, 2001.
Two crystal forms of a helix-rich fatty acid- and retinol-binding protein, Na-FAR-1, from the parasitic nematodeNecator americanus
Authors: Gabrielsen Mads , Rey-Burusco M. Florencia , Griffiths Kate , Roe Andrew J. , Cooper Alan , Smith Brian O. , Kennedy Malcolm W. , Corsico Betina 
Published: June 2012

Na-FAR-1 is an unusual α-helix-rich fatty acid- and retinol-binding protein fromNecator americanus, a blood-feeding intestinal parasitic nematode of humans. It belongs to the FAR protein family, which is unique to nematodes; no structural information is available to date for FAR proteins from parasites. Crystals were obtained with two different morphologies that corresponded to different space groups. Crystal form 1 exhibited space groupP432 (unit-cell parametersa = b = c = 120.80 Å, α = β = γ = 90°) and diffracted to 2.5 Å resolution, whereas crystal form 2 exhibited space groupF23 (unit-cell parametersa = b = c = 240.38 Å, α = β = γ = 90°) and diffracted to 3.2 Å resolution. Crystal form 2 showed signs of significant twinning.