bluuebunny/crossref_metadata_2025_split huggingface dataset:
A critique of current trends in the statistical analysis of seed germination and viability data
Authors: Sileshi Gudeta W. 
Published: March 2012

AbstractStatistical analysis is increasingly used in seed germination/viability studies across different disciplines. The objective of this opinion piece is to assess current trends in statistical analysis of such data, and draw attention of readers to the limitations of the usual inferential statistics in controlling error rates. The assessments are based on a survey of 429 papers published in 139 peer-reviewed journals in the past 11 years. My intention is to identify areas of concern across a wide range of studies. Accordingly, the areas of greatest concern found in the analysis of percentage seed germination and viability data were: (1) pseudoreplication and/or use of a few replicates; (2) ignoring assumptions of ANOVA and non-parametric tests (NPARTs); (3) uncritical data transformation; (4) arbitrary choice of multiple comparison tests; and (5) lack of emphasis on effect sizes. Given the prevalence of these problems, in my opinion we would be building a body of knowledge on a shaky ground. The discussions that follow will: (1) describe situations where germination data violate assumptions of ANOVA and NPARTs; (2) highlight the implications of the various problems to Type I and Type II error rates; and (3) indicate remedial measures based on the recent statistical literature.
Incidence and ecology of very fast germination
Authors: Parsons R.F. 
Published: March 2012

AbstractA group of flowering plant species is known to germinate in less than 24 h from imbibition, but this phenomenon is often overlooked in the current literature. Here, I review this topic by searching the literature published since 1967 and listing the 28 most detailed cases found. Of these, 20 are species of Amaranthaceae (all formerly treated as Chenopodiaceae); 15 of these are from the subfamily Salsoloideae, which is characterized by the possession of spiral embryos. The non-chenopods listed are small numbers of species from the families Acanthaceae, Cruciferae, Gramineae (one species) and Salicaceae (PopulusandSalix). Seeds of the Salsoloideae contain fully differentiated embryos. On imbibition, the embryo cells elongate and the spiral embryo uncoils and ruptures the thin seed coat. This can occur in as little as 10 min. Nearly all of the families showing very fast germination have small to very small seeds and little or no endosperm. Most species have soft, thin seed coats that imbibe water readily. All are from high-stress habitats, either arid or saline or from active floodplains, where they can rapidly exploit temporarily favourable conditions for germination. They exhibit one of two contrasting germination behaviours, either having seeds which all germinate within a very short time of wetting or having seed persistence whereby small amounts of rain cause germination of small fractions of seed from a long-living soil seed bank. Serious confusion in the literature in the use of the term ‘opportunistic’ is pointed out and clarified.
Association of DiGeorge anomaly and caudal dysplasia sequence in a neonate born to a diabetic mother
Authors: Dentici Maria L. , Placidi Silvia , Francalanci Paola , Capolino Rossella , Rinelli Gabriele , Marino Bruno , Digilio Maria C. , Dallapiccola Bruno 
Published: March 2012

AbstractAim/objectiveSeveral studies have demonstrated a significantly increased risk of specific patterns of congenital anomalies in infants born to diabetic mothers. In particular, caudal dysplasia sequence has been linked to pregnancy complicated by maternal diabetes. In addition, several cases of infants born to diabetic mothers presenting with features of DiGeorge anomaly have been reported. Infants with DiGeorge anomaly can display additional manifestations within the spectrum of caudal dysplasia sequence, including vertebral anomalies and renal agenesis.MethodsWe report a neonate presenting with the co-occurrence of features of both DiGeorge anomaly and caudal dysplasia sequence, born to a mother with poorly controlled insulin-dependent diabetes.ResultsThe patient was affected by truncus arteriosus type A1 and hypertrophic cardiomyopathy.ConclusionMaternal diabetes can cause a spectrum of manifestations, expressing with isolated DiGeorge anomaly or caudal dysplasia sequence, with intermediate phenotypes or with the co-occurrence of both the congenital anomalies in the same patient. The present observations argue for a feasible link between truncus arteriosus with hypertrophic cardiomiopathy, DiGeorge anomaly, and maternal diabetes.
Observations of molecular oxygen Atmospheric band emission in the thermosphere using the near infrared spectrometer on the ISS/RAIDS experiment
Authors: Christensen Andrew B. , Yee Jeng‐Hwa , Bishop Rebecca L. , Budzien Scott A. , Hecht James H. , Sivjee Gulamabas , Stephan Andrew W. 
Published: March 2012

Observations of airglow emission using the RAIDS (Remote Atmospheric and Ionospheric Detection System) instruments on the International Space Station Kibo module are reported and compared to a photochemical model of the emission process. Launched in Sept. 2009, RAIDS performed routine observations of the O2(b1Σ → X3Σ) Atmospheric band (O2 A‐band) transition during solar minimum conditions from October 2009 to December 2010. Limb brightness of the (0,0), (0,1) and (1,1) vibration band emissions were measured in the altitude range 80 to 180 km with the Near Infrared Spectrometer (NIRS) instrument, one of eight limb viewing instruments in the RAIDS experiment. Comparison of observed brightness profiles with the model shows very good agreement for the (0,0) and (0,1) bands. The model underestimates the (1,1) brightness profiles throughout the region, especially near the peak. Reasonable variations of composition and selected rate constants do not account for the underestimation of (1,1) band brightness. A contributing factor could be in the assumption of detailed balance and the accepted energy transfer pathways that redistribute energy between the v = 0 and v = 1 states.
Comparison of the bubble and blob distributions during the solar minimum
Authors: Choi H.‐S. , Kil H. , Kwak Y.‐S. , Park Y.‐D. , Cho K.‐S. 
Published: March 2012

Plasma blobs, local plasma density enhancements with respect to the background, in low to middle latitudes are understood as byproducts of equatorial plasma bubbles, but this hypothesis is challenged by observations of blobs in the absence of equatorial bubbles in the same magnetic meridian. This study investigates the causal linkage between bubbles and blobs using their occurrence statistics during the solar minimum. The bubble and blob distributions were obtained by analyzing the ion density data acquired during the period August 2008–April 2010 by the Coupled Ion‐Neutral Dynamics Investigation instrument on board the Communication/Navigation Outage Forecasting System satellite. The seasonal, longitudinal, and latitudinal distributions of bubbles during the solar minimum are similar to those during other periods of the solar cycle. The distinctive bubble distribution during the solar minimum is the high occurrence rate of bubbles after midnight. The blob distribution shows the peak occurrence rate near midnight in the altitude range 400–450 km and around ±25° magnetic latitudes. The bubble occurrence rate is minimal during the June solstice, but the blob occurrence rate is maximal during that season. The blob occurrence rate has a peak value at about a 1700 km magnetic apex height, where the bubble occurrence rate is negligibly small. The difference in the bubble and blob distributions and the frequent occurrence of blobs beyond the bubble apex height suggest that bubbles are not a prerequisite for the creation of blobs.
Folding mechanism of the metastable serpin
α
1
-antitrypsin
Authors: Tsutsui Yuko , Dela Cruz Richard , Wintrode Patrick L. 
Published: March 2012

The misfolding of serpins is linked to several genetic disorders including emphysema, thrombosis, and dementia. During folding, inhibitory serpins are kinetically trapped in a metastable state in which a stretch of residues near the C terminus of the molecule are exposed to solvent as a flexible loop (the reactive center loop). When they inhibit target proteases, serpins transition to a stable state in which the reactive center loop forms part of a six-stranded β-sheet. Here, we use hydrogen-deuterium exchange mass spectrometry to monitor region-specific folding of the canonical serpin human
α
1
-antitrypsin (
α
1
-AT). We find large differences in the folding kinetics of different regions. A key region in the metastable → stable transition, β-strand 5A, shows a lag phase of nearly 350 s. In contrast, the “B-C barrel” region shows no lag phase and the incorporation of the C-terminal residues into β-sheets B and C is largely complete before the center of β-sheet A begins to fold. We propose this as the mechanism for trapping
α
1
-AT in a metastable form. Additionally, this separation of timescales in the folding of different regions suggests a mechanism by which
α
1
-AT avoids polymerization during folding.
Evaporation rate of water in hydrophobic confinement
Authors: Sharma Sumit , Debenedetti Pablo G. 
Published: March 2012

The drying of hydrophobic cavities is believed to play an important role in biophysical phenomena such as the folding of globular proteins, the opening and closing of ligand-gated ion channels, and ligand binding to hydrophobic pockets. We use forward flux sampling, a molecular simulation technique, to compute the rate of capillary evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of gap, surface size, and temperature. Over the range of conditions investigated (gaps between 9 and 14 Å and surface areas between 1 and 9 nm
2
), the free energy barrier to evaporation scales linearly with the gap between hydrophobic surfaces, suggesting that line tension makes the predominant contribution to the free energy barrier. The exponential dependence of the evaporation rate on the gap between confining surfaces causes a 10 order-of-magnitude decrease in the rate when the gap increases from 9 to 14 Å. The computed free energy barriers are of the order of 50
kT
and are predominantly enthalpic. Evaporation rates per unit area are found to be two orders of magnitude faster in confinement by the larger (9 nm
2
) than by the smaller (1 nm
2
) surfaces considered here, at otherwise identical conditions. We show that this rate enhancement is a consequence of the dependence of hydrophobic hydration on the size of solvated objects. For sufficiently large surfaces, the critical nucleus for the evaporation process is a gap-spanning vapor tube.
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography
Authors: Rigort Alexander , Bäuerlein Felix J. B. , Villa Elizabeth , Eibauer Matthias , Laugks Tim , Baumeister Wolfgang , Plitzko Jürgen M. 
Published: March 2012

Cryoelectron tomography provides unprecedented insights into the macromolecular and supramolecular organization of cells in a close-to-living state. However because of the limited thickness range (< 0.5–1 μm) that is accessible with today’s intermediate voltage electron microscopes only small prokaryotic cells or peripheral regions of eukaryotic cells can be examined directly. Key to overcoming this limitation is the ability to prepare sufficiently thin samples. Cryosectioning can be used to prepare thin enough sections but suffers from severe artefacts, such as substantial compression. Here we describe a procedure, based upon focused ion beam (FIB) milling for the preparation of thin (200–500 nm) lamellae from vitrified cells grown on electron microscopy (EM) grids. The self-supporting lamellae are apparently free of distortions or other artefacts and open up large windows into the cell’s interior allowing tomographic studies to be performed on any chosen part of the cell. We illustrate the quality of sample preservation with a structure of the nuclear pore complex obtained from a single tomogram.
Tagging Models for Estimating Survival Rates When Tag Visibility Changes over Time: Partial-Year Tabulation of Recaptures
Authors: Waterhouse Lynn , Hoenig John M. 
Published: March 2012

Abstract
Brownie tagging models are commonly used for estimating survival rates from multiyear tagging studies. The basic model, model 1, assumes that all tags have the same recovery rate. An alternative, model 0, allows newly tagged animals to have a different tag recovery rate than previously tagged animals. This feature might be necessary because new tags are less fouled and more visible than previously applied tags and thus have a higher reporting rate. Model 0 accommodates the different recovery rates through the use of additional parameters, which leads to larger standard errors than in model 1. Model 0′, a new model, also allows newly tagged animals to have a different tag recovery rate than previously tagged ones. It makes use of a known fouling time (the time it takes for tags on newly tagged animals to have the same visibility as tags on previously tagged animals) to divide the year into two parts. During the first part of the year the tags on newly tagged animals are more visible than those on previously tagged ones, while in the second part all tags have the same visibility. Dividing the year into parts and recording the recaptures in each part avoids the failure of the assumption that the reporting rate is constant for all tagged animals, achieves greater precision, and provides estimates of the survival rate at the end of the second year instead of at the end of the third year (as in model 0). The superiority of model 0′ over models 0 and 1 is demonstrated for several cases using Monte Carlo simulation. Simulations were based on the queen conch Strombus gigas fishery of the Turks and Caicos Islands, British West Indies. For that fishery, if the tag reporting rate is altered by 25% or more by fouling, it is beneficial to use model 0′ instead of model 1.
Received January 6, 2011; accepted October 6, 2011
Population Size of Hatchery-Reared and Wild Pallid Sturgeon in the Lower Missouri River
Authors: Steffensen Kirk D. , Powell Larkin A. , Pegg Mark A. 
Published: March 2012

Abstract
The population size of pallid sturgeon Scaphirhynchus albus is currently unknown throughout much of the Missouri River. Listed as federally endangered in 1990, the pallid sturgeon remains one of the rarest fishes in the Missouri and Mississippi River basins, and little to no natural recruitment occurs. Artificial population supplementation via a hatchery propagation program was initiated, necessitating the collection of sexually mature pallid sturgeon. Therefore, the Nebraska Game and Parks Commission maintained an intensive broodstock collection and mark–recapture effort from 2008 to 2010 to capture reproductively ready adults for the propagation program. Coordinated crews fished baited trotlines from the confluence of the Platte and Missouri rivers at river kilometer (rkm) 957.6 to a point about 80.5 rkm downstream. A total of 438 pallid sturgeon were captured, which amounts to a 7.8% recapture rate. The objectives of the study were to (1) use these data to estimate the annual population sizes of wild-origin and hatchery-reared pallid sturgeon within the above-mentioned 80.5-rkm reach of the lower Missouri River and (2) compare current population levels with the Pallid Sturgeon Recovery Team's population objective. We used the mark–recapture data in a robust-design analysis to derive population estimates and annual survival, capture, and temporary emigration rates. The annual population estimate for wild pallid sturgeon varied from 5.4 to 8.9 fish/rkm, whereas the estimate for known hatchery-reared fish varied from 28.6 to 32.3 fish/rkm. The robust-design approach to our analysis resulted in useful estimates of population size and other variables important to quantifying species recovery and management targets; the approach may be suitable for other fisheries management data sets.
Received February 24, 2011; accepted October 13, 2011
Temperature-dependent demagnetization behaviour in perpendicular exchange-coupled SmCo5/FeCo multilayers
Authors: Belemuk A M , Chui S T 
Published: March 2012

Abstract
We study with finite temperature Monte Carlo simulation the temperature-dependent demagnetization behaviour of exchange-coupled multilayers of hard (SmCo5) and soft (FeCo) magnetic materials. The easy axis of the hard phase is perpendicular to the layers, as is motivated by recent experimental results. We perform simulations with and without the dipolar interaction and study the effect of finite temperature on the coercivity, the remanence and the energy density of the composites. We investigate these properties as functions of the soft layer thickness. We find that as the temperature is increased, the increase in the energy product with the addition of soft material becomes progressively smaller than expected because the increase in the remanent magnetization is less than anticipated for two reasons. Because of the different magnetization densities between the hard and the soft phases, magnetic charges are created at the hard–soft boundaries. To reduce the corresponding dipolar energy, at moderate temperatures the magnetization of the soft phase becomes tilted with respect to that of the hard phase; at relatively high temperatures vortex-like structures are created in the soft phase. Furthermore, the addition of soft material reduces the spin wave stiffness and increases the amount of thermal fluctuation. These two effects reduce the rate of increase of the magnetic moment and hence the maximum energy product. At low temperatures, the hysteresis curve shows a two-stage magnetization reversal process. Simulation results for the first instability field H
c1 are in reasonable agreement with theoretical nucleation field H
n estimates for a moderate amount of soft materials. The difference between H
c1 and H
n when the amount of soft material is small is explained. As the temperature is increased, the two-stage process disappears, most likely due to the formation of vortex-like structures in the soft phase.
Development of polymer MEMS process technology as an approach to a sustainable production system
Authors: Sugiyama Susumu , Amaya Satoshi , Viet Dao Dzung 
Published: March 2012

Abstract
Polymethyl methacrylate (PMMA) has been proposed as a material for micro-electromechanical systems (MEMS) to initiate the research on environmentally friendly micro-nano machining technology using polymer materials. A polymer MEMS process has been developed using hot embossing and precision machining. MEMS structures less than 2 μm were successfully embossed. The PMMA layer that remained after hot embossing was removed by a polishing process to release the movable parts. A PMMA electrostatic comb-drive microactuator was fabricated. Both finger width and gap between fingers were 5 μm, and thickness was larger than 70 μm. An operated displacement of 11 μm at a drive voltage of 100 V was obtained. It was 20 times larger than that of an identical silicon device. A torsional micro mirror device driving with vertical comb actuator was fabricated. The size of the mirror was 1×1 mm
2. The maximum tilt angle of 5.6 was obtained with driving voltage of 100 V and frequency up to 100 Hz. A chevron-shaped PMMA thermal actuator with a thickness of about 50 μm has been fabricated and tested successfully. The displacement was about 5 times larger than that of a Si counterpart at the same power consumption.
Fabrication and properties of terbium phosphate nanorods
Authors: Tran Thu Huong , Tran Kim Anh , Hoang Thi Khuyen , Pham Thu Hien , Le Quoc Minh 
Published: March 2012

Abstract
Recently, luminescent nanomaterials with one-dimensional (1D) structured form have been extensively investigated as fluorescent label agents in biology. Among them, 1D nanostructured terbium compounds (for example terbium phosphate) have attracted great attention due to their high-emission efficiency in water. In this report, terbium phosphate nanorods were successfully prepared by hydrothermal method in autoclave for the first time. This method is a simple one, which permits obtaining large-scale, uniform and pure product. The size of the rods can be controlled precisely. The nanorods have diameters from 15 to 50 nm, and lengths from 300 to 500 nm. Based on the effects of change of pH values to the size, crystalline structure and morphology of terbium phosphate nanorods, field emission scanning electron microscopy (FE-SEM) and x-ray diffraction (XRD) data of the as-synthesized samples have been elucidated. The photoluminescent (PL) spectra of TbPO
4 nanorods have been measured at room temperature under ultraviolet excitation and show four high luminescence main peaks at 490, 545, 585 and 620 nm.
Promising option in the prevention of idiopathic anaphylaxis: Omalizumab
Authors: DEMIRTÜRK Mustafa , GELINCIK Asli , ÇOLAKOĞLU Bahattin , DAL Murat , BÜYÜKÖZTÜRK Suna 
Published: March 2012

AbstractAnaphylaxis is a serious and probably lethal systemic reaction which occurs instantaneously after exposure to an allergen. It can occur after exposure to various triggers including allergic and non‐allergic factors. When a trigger cannot be determined, idiopathic anaphylaxis is considered. In idiopathic anaphylaxis presenting with frequent attacks, long‐term prophylaxis with H1 antihistamine and steroid treatment are recommended. Omalizumab, a humanized monoclonal antibody drug which decreases free immunoglobulin E molecules in the circulation, is approved for the treatment of chronic severe persistent allergic asthma. We report a 46‐year‐old female patient with severe uncontrolled allergic asthma and idiopathic anaphylaxis presenting with attacks of abdominal pain, generalized urticaria, feeling of strangulation in her throat and unconsciousness. Omalizumab at a dose of 375 mg once every 2 weeks was administrated and at the end of 3 months anaphylactic attacks had ceased. At the end of the sixth month of omalizumab therapy, her injection intervals were extended to 4 weeks. After she began experiencing moderate attacks of urticaria and hoarsening, however, initial treatment plan was reestablished. Currently, she has completed her first year of treatment without further attacks.
The effect of experimental warming and precipitation change on proteolytic enzyme activity: positive feedbacks to nitrogen availability are not universal
Authors: Brzostek Edward R. , Blair John M. , Dukes Jeffrey S. , Frey Serita D. , Hobbie Sarah E. , Melillo Jerry M. , Mitchell Robert J. , Pendall Elise , Reich Peter B. , Shaver Gaius R. , Stefanski Artur , Tjoelker Mark G. , Finzi Adrien C. 
Published: March 2012

AbstractNitrogen regulates the Earth's climate system by constraining the terrestrial sink for atmospheric CO2. Proteolytic enzymes are a principal driver of the within‐system cycle of soil nitrogen, yet there is little to no understanding of their response to climate change. Here, we use a single methodology to investigate potential proteolytic enzyme activity in soils from 16 global change experiments. We show that regardless of geographical location or experimental manipulation (i.e., temperature, precipitation, or both), all sites plotted along a single line relating the response ratio of potential proteolytic activity to soil moisture deficit, the difference between precipitation and evapotranspiration. In particular, warming and reductions in precipitation stimulated potential proteolytic activity in mesic sites – temperate and boreal forests, arctic tundra – whereas these manipulations suppressed potential activity in dry grasslands. This study provides a foundation for a simple representation of the impacts of climate change on a central component of the nitrogen cycle.