bluuebunny/crossref_metadata_2025 huggingface dataset:
VI.—On the English Origin of Gothic Architecture
Authors: Parker John Henry
Published: January 2012

My object on the present occasion is to call attention to what appears to be a popular delusion on a subject of considerable importance to the archaeologist. If it is not entirely a delusion, it is certainly a great exaggeration and misapprehension. And yet it is almost an article of faith with every Frenchman; and it has so long been accepted by German and English antiquaries as an ascertained fact that it will seem like heresy to doubt it—I mean the opinion that the medieval style of architecture usually called “the Gothic style ” is of French origin, and that Suger, Abbat of St.-Denis, near Paris, was the inventor, and the church of St.-Denis the first example, of it. The subject, in all its bearings, has been my favourite study for the last thirty years, and this particular church I have visited very often, and carefully examined on different occasions in company with some of the best-informed French antiquaries and architects, including the very able architect M. Viollet Le Due, who has charge of the works there.
XII.—Inventories and Valuations of Religious Houses at the time of the Dissolution, from the Public Record Office
Authors: Walcott Mackenzie E. C.
Published: January 2012

Among the scarcest illustrations of monastic arrangement are original ground plans, such as those of Canterbury, Chester, the Charter House, and Tynemouth, with descriptions of a later date in the Rites of Durham. Next in value are inventories in detail, as in the case of Christ Church (Hants), Bridlington, and Tewkesbury; these also are extremely rare, but I have been able to add to them those of Whalley Abbey, Stanlaw, St. Martin's Newark, Dover and the Maison Dieu in the same town, Minster in the Isle of Sheppey, St. Osyth's (Essex), and St. Alban's, in the time of Edward VI.
XVI.—Observations on the Question of the Spot at which Cæsar landed, as affected by the Communication received from the Admiralty on the Tides in the Channel
Authors: Airy G. B.
Published: January 2012

Having been invited to address to the Society any remarks which might occur to me on the subject of the communication from the Admiralty, I would first observe that the result of this investigation proves the great advantage of the course pursued by the President and Council, namely, that of referring to official authority for the determination of critical points applying to the question at issue. The Society have expressed so fully their sense of the liberality and courtesy of the First Lord and the Board of Admiralty, and the care bestowed on this matter by the Hydrographer, that it is needless for me to speak on that subject. I will therefore proceed to advert lightly to the history of these investigations, and state how the hydrographical inquiry undertaken by the Admiralty bears upon the matter.
XXII. Two Rolls of Arms of the Reign of King Edward the First; with some Prefatory Remarks
Authors: Perceval Charles Spencer
Published: January 2012

The first of the two following rolls, the entire blazon of which has never before appeared in print, has for many years been preserved in the Library of the Society of Antiquaries. How or when it came into their possession does not appear, and the only fact that has been ascertained as to its previous history is, that about the year 1610 it was in the custody of Nicholas Charles, then Lancaster Herald, to whose pains we owe the preservation of the second roll, known of late by his name, and now also published for the first time.
III.—Further Observations on the Primitive Site, Extent, and Circumvallation of Roman London
Authors: Black William Henry
Published: January 2012

In the discussion which took place on the reading of my former paper on this subject, on the 26th of November last, remarks were made which want of time prevented me from answering. I now, therefore, propose to lay before the Society some of my further thoughts on this subject, and, first, to answer some of those remarks.
VIII.—On the Centuriation of Roman Britain
Authors: Coote Henry Charles
Published: January 2012

The civilization which Western Europe received at the hands of Rome was due in great part to the colonies planted by her in every subjected portion of it. It may, therefore, be neither trivial nor uninteresting to inquire whether that colonisation extended itself and its benefits to this country also. Throughout the history of Rome conquest preceded colonisation. The land of a conquered nation, if the Roman government insisted upon its right, became the absolute property of the Roman people. Belonging from that time to the State, it could be retained by the Government as public property (i. e. in fact and etymology the property of the people,) to be used for the support and relief of the finances, or it could, by an act of the Legislature, be granted and appropriated to private individuals, of course a portion of that people or their privileged allies.
XI.—On the English medieval drinking bowls called Mazers
Authors: Hope W.H. St. John
Published: January 2012

Of all the drinking vessels in use from the thirteenth to the sixteenth centuries, none were so common and so much prized as those known to us as mazers. They occur in numerous wills and inventories under various names, such as ciphi or cuppae de mazero or de murra, mazeri, ciphi murrei, mazerei, hanaps de maser, and later as murrae and mazers, etc., on the derivations of which much valuable matter has been written. But, under whatever name it appears, it is quite clear that the same vessel is meant, viz. a drinking bowl turned out of some kind of wood, but by preference of maple, and especially the spotted or speckled variety which we call bird's-eye maple.
XXII.—A Brief Account of a Small Portrait of Mary Queen of Scots; preserved at Osborne House, in the Isle of Wight. Addressed to John Evans, Esq., President
Authors: Scharf George
Published: January 2012

Dear Mr. President,—Whilst endeavouring to collect and arrange the portraits of Mary queen of Scots on which reliance can be placed, my attention was drawn to an engraving taken from a picture representing her, during the period of her residence in France, at full length, standing by a chair, and wearing a long gown and small cap and feather.
IV.—On some remarkable ecclesiastical figures in the cathedral church of Wells
Authors: Hope W.H. St. John
Published: January 2012

The cathedral church of Wells contains, both within and without, a number of ecclesiastical figures of unusual interest. Besides a series of seven effigies of early bishops, all carved at the same time about the end of the twelfth century, there are, in addition to the well-known incised slab of bishop William de Bitton II. 1267-1274, five effigies of pre-reformation bishops, viz.: William de Marchia, 1293-1302; John de Drokensford, 1309-1329; Ralph de Salopia, 1329-1363; John Harewell 1369-1386; Thomas de Bekinton, 1443-1465. The last-named has also a cadaver below. There are, besides, effigies of two seventeenth century bishops, John Still, 1593-1608, and Robert Creighton, 1670-1672.
II.—Some Account of Ancient Oaken Coffins discovered on the lands adjoining Featherstone Castle, near Haltwhistle, Northumberland
Authors: Snagge Thomas William
Published: January 2012

In the year 1825 some labourers who were employed in draining a swampy field upon a farm belonging to the Featherstone Castle estate came upon what seemed to be part of the trunk of an oak-tree. Finding that it impeded the progress of their work they endeavoured to cut it out with an axe, when to their surprise they discovered that the trunk was hollowed and contained some human bones, which, however, speedily became dust when exposed to the air. Proceeding with their work they found the remains of four more coffins of the same kind, in one of which was part of a skull.
XVI.—On an Early French Deed, A.D. 1397, relating to the Knights of St. John of Jerusalem
Authors: Peacock Edward , Watson C. Knight
Published: January 2012

In calling the attention of the Society to the interesting deed exhibited this evening by our Fellow, Mr. Peacock, it would be superfluous to do more than allude in a most cursory manner to the early history and general organization of the famous order of the Knights Hospitallers to which it relates. I need but refer to the General Chapter held at Montpellier in 1329—the date of the deed before us is 1397—when Elyan de Villanova was Grand Master, and at which the Order was for the first time divided into the seven ‘Languages,’ as they were called, of France, Provence, Auvergne, Italy, Germany, England, and Aragon; a number which was afterwards raised to eight by the addition of Castille and Portugal as a single ‘Language.’ The ‘Language’ of France, I may add, was divided into three Grand Priories: the Priory of France, which contained forty-five Commanderies–the name given to the estate of the Order placed under the control of one of the brothers, called a Commander—the Priory of Aquitaine, which contained sixty-five, and the Priory of Champagne, which contained twenty-four. On the system on which, in the fourteenth century, the property of the fraternity was managed, and its income derived and expended in England, the fullest light has been thrown by the very valuable report of the English Prior Philip de Thame to the Grand Master already mentioned, Elyan de Villanova, for the year 1338, edited for the Camden Society, in 1857, by the Rev. Lambert B. Larking, with an Historical Introduction by Mr. John Mitchell Kemble. No such information however, so far as I am aware, exists in print relating to the fraternity in France, and this circumstance gives to the deed before us an importance which at a first glance it might not be held to possess. For, although in its general features the system which regulated the Priories in different countries at the same periods was probably in substance the same, still we should be justified in inferring a priori that differences of detail must necessarily have arisen from the varieties of custom, of character, and of social condition, which marked the people with whom they were brought into contact. And in point of fact any one who is familiar with the publication of the Camden Society will find as he reads this deed that this à priori conjecture is borne out by the result, the general drift of which is to show the greater servitude to which the peasantry and lower orders generally were subjected in France, as contrasted with the comparative freedom enjoyed in this country.
XIX.—Note on an Anglo-Saxon Knife, found in Kent, bearing an Inscription
Authors: Evans John
Published: January 2012

By the kindness of Mr. Edward Lloyd of the Winns, Walthamstow, I am enabled to exhibit a very remarkable Anglo-Saxon knife lately found in excavating for the foundations of a house which he is building at Sittingbourne, Kent.

In general form the knife is of a well-known type, and closely resembles one found in Lad Lane in the city of London, and engraved by Mr. C. Roach Smith in his Collectanea Antiqua. The total length is 12¾ inches, and the extreme breadth 1⅜ inch. The tang for insertion in the handle is 3½ inches long, and there is a shoulder at its junction with the blade both at the back and the edge.
XXIII.—On the Crypt of the Chapter House, Westminster Abbey
Authors: Harrod Henry
Published: January 2012

Beneath the Chapter House at Westminster is a Crypt of so remarkable a character that it is surprising no efforts should have been made to ascertain the purpose of its construction, or, if such efforts have been made, that they should have produced no result.
V.—Roger of Salisbury, first bishop of Bath and Wells, 1244-1247
Authors: Church C.M.
Published: January 2012

The episcopate of Roger of Salisbury, first bishop who bore the title of Bath and Wells, is short, but memorable in the annals of the church of Wells.

It was the time when the rule of election of the bishop by the joint action of the two chapters of the monks of Bath and the canons of Wells was authoritatively and finally settled, and the style of the bishop, Episcopus Bathoniensis et Wellensis, was officially adopted.
XVII. Remarks on some early Churches in France and Switzerland, partly of the time of Charlemagne. Communicated by J. H. Parker, Esq., F.S.A.; in a Letter addressed to the Right Honourable the Earl Stanhope, President
Authors: Parker J. H.
Published: January 2012

In the series of letters I have hitherto had the honour of addressing to your Lordship, and of reading before this Society, I have confined myself to the topographical arrangement, merely following the order of my own actual tours in the English provinces of France, which were originally undertaken with a view of ascertaining whether there was any English character in the architecture of these provinces, or any marked connection between them and the architecture of England of the same period. I purposely omitted Normandy, as having been previously well described by Mr. Gally Knight and others, although that province is more familiar to me than any other part of France, and I have notes of many buildings there of which, to the best of my knowledge, no accounts have been published; but, as I fear that mere topographical descriptions of buildings are always rather dry and uninteresting, I propose on the present occasion to give some account of certain very early churches in different parts of France and Switzerland, which I have selected on account of their peculiarity, without reference to their topographical situation.
XIV.—Excavations on the site of the Roman city at Silchester, Hants, in 1891; with a Note on the animal remains found during the excavations
Authors: Fox George E. , Jones Herbert
Published: January 2012

The plan of operations decided upon last year has been pursued without change during the season just past. It may be remembered that Insula I., partly explored in 1890, is traversed at its southern extremity by a modern road, which passes completely across the site of the city. All the ground to the north of this road was examined last year, but the small section south of it still remained untouched. One task was, therefore, to complete our researches in Insula I.; the other, there being ample funds for the purpose, to work out two more insulæ.
I.—The “Ritual Ordinance” of Neophytus
Authors: Warren Frederick Edward
Published: January 2012

The manuscript which forms the subject of this communication is a small quarto volume, consisting at present of eighty-five leaves, six and a half inches long and five inches broad, the property of Mr. David Laing, the Librarian of the Signet Library at Edinburgh.
XIII.—Some Notarial Marks in the “Common Paper” of the Scriveners' Company
Authors: Freshfield Edwin
Published: January 2012

The main object of this paper is to exhibit to the Fellows a collection of the Notarial Marks used by the notarial members of the Scriveners' Company of London.

These marks are preserved in a book called the “Common Paper” of the Scriveners' Company, which is in fact the register of members of the Company from the year 1390 to the year 1628.
XXII.—On the Discovery of some Remains of the Chapter-house of Beverley Minster
Authors: Bilson John
Published: January 2012

The remains which are the subject of these notes are, unfortunately, but scanty, and belong to the undercroft of the chapter-house, rather than to the chapter-house itself. Still, slight as they are, they enable us to determine with sufficient accuracy the plan of what must have been a beautiful addition to this most beautiful church.
Availability of snacks, candy and beverages in hospital, community clinic and commercial pharmacies
Authors: Whitehouse Anne , Simon Anna , French Simone A , Wolfson Julian
Published: January 2012

Objective

The purpose of the present study was to measure the availability of energy-dense foods and sugar-sweetened beverages in pharmacies and to examine differences by pharmacy type and presence of a food policy.

Design

Trained research staff visited pharmacies (n 37) to measure shelf space and variety of snacks, candy and sugar-sweetened beverages available within 10 ft (3·05 m) of the pharmacy register.

Setting

Community clinic, hospital and commercial pharmacies in Minneapolis, MN, USA.

Subjects

Employees were interviewed regarding pharmacy food policies.

Results

Approximately 60 % of pharmacies had foods and/or sugar-sweetened beverages available for purchase within 10 ft (3·05 m) of the pharmacy register. Total shelf space (P = 0·02) and variety (P = 0·0003) differed significantly by pharmacy type and were greatest among community clinic pharmacies. Over half of pharmacies had no food policy (58·3 %). Pharmacies with food policies were less likely to have foods/beverages available within 10 ft (3·05 m) of the pharmacy register than pharmacies with no food policies (P = 0·03).

Conclusions

Candy, snacks and sugar-sweetened beverages are highly available in the pharmacy environment. Presence of a policy is associated with less food availability within 10 ft (3·05 m) of the pharmacy register and represents an important potential intervention strategy.
Selective breeding for helplessness in rats alters the metabolic profile of the hippocampus and frontal cortex: a 1H-MRS study at 9.4 T
Authors: Schulz Daniela , Smith David , Yu Mei , Lee Hedok , Henn Fritz A.
Published: January 2012

In humans metabolic changes, particularly in frontal areas of the brain, accompany depressive disorders, but few studies were conducted in animal models of depression. We used hydrogen-1 magnetic resonance spectroscopy at 9.4 T to measure the metabolic profiles of the hippocampus and frontal cortex in congenital learned helpless (cLH) and wild-type (WT) rats. The learned helplessness model of depression exposes animals to uncontrollable stress to induce changes in emotion, cognition and behaviour, but cLH rats were selectively bred to show changes in behaviour even without exposure to uncontrollable stress. Experimentally naive male 8- to 10-wk-old cLH (n = 10) and WT rats (n = 22) underwent spectroscopy and were exposed to uncontrollable stress 1 wk after the scan. We found that cLH compared to WT rats had lower levels of glutamate in the hippocampus and lower levels of choline-containing compounds in the hippocampus and frontal cortex, but higher levels of taurine and phosphocreatine in these regions, pointing to compensatory efforts of the brain to reduce excitotoxic potential and to increase neuroprotection and energy, possibly as a result of cellular stress and damage. The reduction in choline-containing phospholipids might represent a source or correlate of such stress. Overall, the results indicate that metabolic abnormalities are present in animals with a predisposition to helplessness even without exposure to explicit stress and may help identify non-invasive biomarkers in individuals who are prone to depression.
COGNITIVE ECONOMICS AND THE LOGIC OF ABDUCTION
Authors: WOODS JOHN
Published: January 2012

An agent-centered, goal-directed, resource-bound logic of human reasoning would do well to note that individual cognitive agency is typified by the comparative scantness of available cognitive resources—information, time, and computational capacity, to name just three. This motivates individual agents to set their cognitive agendas proportionately, that is, in ways that carry some prospect of success with the resources on which they are able to draw. It also puts a premium on cognitive strategies which make economical use of those resources. These latter I callscant-resource adjustment strategies,and they supply the context for an analysis of abduction. The analysis is Peircian in tone, especially in the emphasis it places on abduction’signorance-preservingcharacter. My principal purpose here is to tie abduction’s scarce-resource adjustment capacity to its ignorance preservation.
Response of the polar magnetic field intensity to the exceptionally high solar wind streams in 2003
Authors: Lukianova Renata , Mursula Kalevi , Kozlovsky Alexander
Published: January 2012

The exceptionally high solar wind stream activity in 2003 caused a record intensity in the auroral electrojet currents, leading to a major reduction of the horizontal field at auroral latitudes and to a notable strengthening of the vertical geomagnetic field in the polar cap. This strengthening is clearly visible in the observatory annual values as a significant deflection in the corresponding secular variation. A similar but weaker deflection also occurs during the strongest high speed stream years of the earlier solar cycles, e.g., in 1983 and 1994. We also found that, in addition to the disturbed times, the westward electrojet was often enhanced even during the most quiet times of the strongest high speed stream years. The quiet time level was more disturbed in 2003 than in other high speed stream years, when an exceptionally clear signal was seen in the polar cap Z intensity even in the annual mean curve in this year. We exclude other current systems like the ring current or the DPY current as possible explanations.
Reconciling two approaches to attribution of the 2010 Russian heat wave
Authors: Otto F. E. L. , Massey N. , van Oldenborgh G. J. , Jones R. G. , Allen M. R.
Published: January 2012

In the summer 2010 Western Russia was hit by an extraordinary heat wave, with the region experiencing by far the warmest July since records began. Whether and to what extent this event is attributable to anthropogenic climate change is controversial. Dole et al. (2011) report the 2010 Russian heat wave was “mainly natural in origin” whereas Rahmstorf and Coumou (2011) write that with a probability of 80% “the 2010 July heat record would not have occurred” without the large‐scale climate warming since 1980, most of which has been attributed to the anthropogenic increase in greenhouse gas concentrations. The latter explicitly state that their results “contradict those of Dole et al. (2011).” Here we use the results from a large ensemble simulation experiment with an atmospheric general circulation model to show that there is no substantive contradiction between these two papers, in that the same event can be both mostly internally‐generated in terms of magnitude and mostly externally‐driven in terms of occurrence‐probability. The difference in conclusion between these two papers illustrates the importance of specifying precisely what question is being asked in addressing the issue of attribution of individual weather events to external drivers of climate.
Does proxy uncertainty affect the relations inferred between the Pacific Decadal Oscillation and wildfire activity in the western United States?
Authors: Kipfmueller Kurt F. , Larson Evan R. , St. George Scott
Published: January 2012

We examined a set of five proxy reconstructions of the Pacific Decadal Oscillation (PDO) to test whether the choice of reconstruction affected the association between the PDO and widespread forest fires in the western United States. Exact binomial tests suggest the PDO has little direct impact on wildfires, with a statistically‐significant association between the phase of the PDO and regional fire activity observed with only one reconstruction. Region‐wide fires were not consistently associated with specific phase combinations of ENSO and the PDO. Any conclusion that extensive wildfires are more or less common when the PDO is in one phase or the other depends entirely on the choice of PDO reconstruction. Without a better understanding of low‐frequency behavior in the north Pacific prior to 1900, efforts using proxy data to determine whether or not the PDO affects wildfire activity in the western United States will produce ambiguous results.
A new, high‐resolution surface mass balance map of Antarctica (1979–2010) based on regional atmospheric climate modeling
Authors: Lenaerts J. T. M. , van den Broeke M. R. , van de Berg W. J. , van Meijgaard E. , Kuipers Munneke P.
Published: January 2012

A new, high resolution (27 km) surface mass balance (SMB) map of the Antarctic ice sheet is presented, based on output of a regional atmospheric climate model that includes snowdrift physics and is forced by the most recent reanalysis data from the European Centre for Medium‐Range Weather Forecasts (ECMWF), ERA‐Interim (1979–2010). The SMB map confirms high accumulation zones in the western Antarctic Peninsula (>1500 mm y−1) and coastal West Antarctica (>1000 mm y−1), and shows low SMB values in large parts of the interior ice sheet (<25 mm y−1). The location and extent of ablation areas are modeled realistically. The modeled SMB is in good agreement with ±750 in‐situ SMB measurements (R = 0.88), without a need for post‐calibration. The average ice sheet‐integrated SMB (including ice shelves) is estimated at 2418 ± 181 Gt y−1. Snowfall shows modest interannual variability (σ = 114 Gt y−1), but a pronounced seasonal cycle (σ = 30 Gt mo−1), with a winter maximum. The main ablation process is drifting snow sublimation, which also peaks in winter but with little interannual variability (σ = 9 Gt y−1).
Electromagnetic wave propagation in general relativistic situations: A general solution of the problem
Authors: Ferencz Csaba
Published: January 2012

The exact full‐wave modeling and computation of the electromagnetic signals propagating through curved space‐time is important from theoretical and practical aspects (e.g., for satellite positioning systems). In this paper a general solution method is presented for these problems. Beside this, it is demonstrated that the Method of Inhomogeneous Basic Modes is a natural consequence of Maxwell's equations in the general relativity.
Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips
Authors: Cooper Donald , Callahan Bryan , Callahan Phil , Burnett Lee
Published: January 2012

Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. These data were then used to create standard curves to allow quantification of COC/BE in biological samples. MIR quantification of COC and BE proved to be a sensitive, economical, and faster alternative to more costly methods, such as gas chromatography-mass spectrometry, tandem mass spectrometry, or high pressure liquid chromatography. MIR is a valuable tool that provides instant data acquisition, tracking and analysis for the emerging field of mobile platform informatics (MPI).
SBGN PD: Current status, future changes and unresolved issues.
Authors: Moodie Stuart
Published: January 2012

The presentations reports and the current status of the SBGN-PD specification and highlights issues for further discussion.
Dynamical cage behaviour and hydrogen migration in hydrogen and hydrogen-tetrahydrofuran clathrate hydrates
Authors: Gorman Paul D. , English Niall J. , MacElroy J. M. D.
Published: January 2012

Classical equilibrium molecular dynamics simulations have been performed to investigate dynamical properties of cage radial breathing modes and intra- and inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen–tetrahydrofuran sII hydrates at 0.05 kbar and up to 250 K. For the mixed H2–THF system in which there is single H2 occupation of the small cage (labelled “1SC 1LC”), we find that no H2 migration occurs, and this is also the case for pure H2 hydrate with single small-cavity occupation and quadruple occupancy for large cages (dubbed “1SC 4LC”). However, for the more densely filled H2–THF and pure-H2 systems, in which there is double H2 occupation in the small cage (dubbed “2SC 1LC” and “2SC 4LC,” respectively), there is an onset of inter-cage H2 migration events from the small cages to neighbouring cavities at around 200 K, with an approximate Arrhenius temperature-dependence for the migration rate from 200 to 250 K. It was found that these “cage hopping” events are facilitated by temporary openings of pentagonal small-cage faces with the relaxation and reformation of key stabilising hydrogen bonds during and following passage. The cages remain essentially intact up to 250 K, save for transient hydrogen bond weakening and reformation during and after inter-cage hydrogen diffusion events in the 200–250 K range. The “breathing modes,” or underlying frequencies governing the variation in the cavities’ radii, exhibit a certain overlap with THF rattling motion in the case of large cavities, while there is some overlap of small cages’ radial breathing modes with lattice acoustic modes.
Transport coefficients of the TIP4P-2005 water model
Authors: Rozmanov Dmitri , Kusalik Peter G.
Published: January 2012

A detailed understanding of the dynamics of liquid water at molecular level is of fundamental importance as well as have applications in many branches of science and technology. In this work, the diffusion of the TIP4P-2005 model of water is systematically investigated in liquid phase in the temperature range 210–310 K. The translational and rotational diffusions, as well as correlations between them, are examined. The effects of system size and shape are also probed in this study. The results suggest the presence of a temperature of dynamical arrest of molecular translations in the range of 150–180 K and of molecular rotations in the range of 80–130 K, depending on specific direction. A substantial change in the preferred directions of translations and rotations relative to the molecular coordinate system is observed slightly below (≈15 K) the melting temperature of the model. It is shown that there is a correlation between translational and rotational molecular motions essential for diffusion in the liquid. The presence of hydrodynamic size effects is confirmed and quantified; it is also shown that using a non-cubic simulation box for a liquid system leads to an anisotropic splitting in the diffusion tensor. The findings of this study enhance our general understanding of models of water, specifically the TIP4P-2005 model, as well as provide evidences of the direct connection between thermodynamics of liquid water and dynamics of its molecules.
Transforming graphite to nanoscale diamonds by a femtosecond laser pulse
Authors: Nüske R. , Jurgilaitis A. , Enquist H. , Harb M. , Fang Y. , Håkanson U. , Larsson J.
Published: January 2012

Formation of cubic diamond from graphite following irradiation by a single, intense, ultra-short laser pulse has been observed. Highly oriented pyrolytic graphite (HOPG) samples were irradiated by a 100 fs pulse with a center wavelength of 800 nm. Following laser exposure, the HOPG samples were studied using Raman spectroscopy of the sample surface. In the laser-irradiated areas, nanoscale cubic diamond crystals have been formed. The exposed areas were also studied using grazing incidence x-ray powder diffraction showing a restacking of planes from hexagonal graphite to rhombohedral graphite.
Ferric, not ferrous, heme activates RNA-binding protein DGCR8 for primary microRNA processing
Authors: Barr Ian , Smith Aaron T. , Chen Yanqiu , Senturia Rachel , Burstyn Judith N. , Guo Feng
Published: January 2012

The RNA-binding protein DiGeorge Critical Region 8 (DGCR8) and its partner nuclease Drosha are essential for processing of microRNA (miRNA) primary transcripts (pri-miRNAs) in animals. Previous work showed that DGCR8 forms a highly stable and active complex with ferric [Fe(III)] heme using two endogenous cysteines as axial ligands. Here we report that reduction of the heme iron to the ferrous [Fe(II)] state in DGCR8 abolishes the pri-miRNA processing activity. The reduction causes a dramatic increase in the rate of heme dissociation from DGCR8, rendering the complex labile. Electronic absorption, magnetic circular dichroism, and resonance Raman spectroscopies indicate that reduction of the heme iron is accompanied by loss of the cysteines as axial ligands. ApoDGCR8 dimers, generated through reduction and removal of the heme, show low levels of activity in pri-miRNA processing in vitro. Importantly, ferric, but not ferrous, heme restores the activity of apoDGCR8 to the level of the native ferric complex. This study demonstrates binding specificity of DGCR8 for ferric heme, provides direct biochemical evidence for ferric heme serving as an activator for miRNA maturation, and suggests that an intracellular environment increasing the availability of ferric heme may enhance the efficiency of pri-miRNA processing.
Host RNAs, including transposons, are encapsidated by a eukaryotic single-stranded RNA virus
Authors: Routh Andrew , Domitrovic Tatiana , Johnson John E.
Published: January 2012

Next-generation sequencing is a valuable tool in our growing understanding of the genetic diversity of viral populations. Using this technology, we have investigated the RNA content of a purified nonenveloped single-stranded RNA virus, flock house virus (FHV). We have also investigated the RNA content of virus-like particles (VLPs) of FHV and the related
Nudaurelia capensis
omega virus. VLPs predominantly package ribosomal RNA and transcripts of their baculoviral expression vectors. In addition, we find that 5.3% of the packaged RNAs are transposable elements derived from the Sf21 genome. This observation may be important when considering the therapeutic use of VLPs. We find that authentic FHV virions also package a variety of host RNAs, accounting for 1% of the packaged nucleic acid. Significant quantities of host messenger RNAs, ribosomal RNA, noncoding RNAs, and transposable elements are readily detected. The packaging of these host RNAs elicits the possibility of horizontal gene transfer between eukaryotic hosts that share a viral pathogen. We conclude that the genetic content of nonenveloped RNA viruses is variable, not just by genome mutation, but also in the diversity of RNA transcripts that are packaged.
Bright illusions reduce the eye's pupil
Authors: Laeng Bruno , Endestad Tor
Published: January 2012

We recorded by use of an infrared eye-tracker the pupil diameters of participants while they observed visual illusions of lightness or brightness. Four original illusions {based on Gaetano Kanisza's [Kanizsa G (1976) Subjective contours.
Sci Am
234:48–52] and Akiyoshi Kitaoka's [Kitaoka A. (2005)
Trick Eyes
(Barnes & Noble, New Providence, NJ).] examples} were manipulated to obtain control conditions in which the perceived illusory luminance was either eliminated or reduced. All stimuli were equiluminant so that constrictions in pupillary size could not be ascribed to changes in light energy. We found that the pupillary diameter rapidly varied according to perceived brightness and lightness strength. Differences in local contrast information could be ruled out as an explanation because, in a second experiment, the observers maintained eye fixation in the center of the display; thus, differential stimulation of the fovea by local contrast changes could not be responsible for the pupillary differences. Hence, the most parsimonious explanation for the present findings is that pupillary responses to ambient light reflect the perceived brightness or lightness of the scene and not simply the amount of physical light energy entering the eye. Thus, the pupillary physiological response reflects the subjective perception of light and supports the idea that the brain's visual circuitry is shaped by visual experience with images and their possible sources.
Optically monitoring voltage in neurons by photo-induced electron transfer through molecular wires
Authors: Miller Evan W. , Lin John Y. , Frady E. Paxon , Steinbach Paul A. , Kristan William B. , Tsien Roger Y.
Published: January 2012

Fluorescence imaging is an attractive method for monitoring neuronal activity. A key challenge for optically monitoring voltage is development of sensors that can give large and fast responses to changes in transmembrane potential. We now present fluorescent sensors that detect voltage changes in neurons by modulation of photo-induced electron transfer (PeT) from an electron donor through a synthetic molecular wire to a fluorophore. These dyes give bigger responses to voltage than electrochromic dyes, yet have much faster kinetics and much less added capacitance than existing sensors based on hydrophobic anions or voltage-sensitive ion channels. These features enable single-trial detection of synaptic and action potentials in cultured hippocampal neurons and intact leech ganglia. Voltage-dependent PeT should be amenable to much further optimization, but the existing probes are already valuable indicators of neuronal activity.
The prospect for fuel ion ratio measurements in ITER by collective Thomson scattering
Authors: Stejner M. , Korsholm S. B. , Nielsen S. K. , Salewski M. , Bindslev H. , Furtula V. , Leipold F. , Michelsen P. K. , Meo F. , Moseev D.
Published: January 2012

We show that collective Thomson scattering (CTS) holds the potential to become a new diagnostic principle for measurements of the fuel ion ratio, n
T/n
D, in ITER. Fuel ion ratio measurements will be important for plasma control and machine protection in ITER. Measurements of ion cyclotron structures in CTS spectra have been suggested as the basis for a new fuel ion ratio diagnostic which would be well suited for reactor environments and capable of providing spatially resolved measurements in the plasma core. Such measurements were demonstrated in recent experiments in the TEXTOR tokamak. Here we conduct a sensitivity study to investigate the potential measurement accuracy of a CTS fuel ion ratio diagnostic on ITER. The study identifies regions of parameter space in which CTS can be expected to provide useful information on plasma composition, and we find that a CTS fuel ion ratio diagnostic could meet the ITER measurement requirements for a standard ELMy H-mode discharge.
RFX-mod wall conditioning by lithium pellet injection
Authors: Munaretto S. , Dal Bello S. , Innocente P. , Agostini M. , Auriemma F. , Barison S. , Canton A. , Carraro L. , De Masi G. , Fiameni S. , Scarin P. , Terranova D.
Published: January 2012

Plasma–wall interaction is one of the most important issues that present magnetic confinement devices have to face. In the RFX-mod reversed field pinch experiment plasma–wall interaction has become a hard point increasing plasma current up to the RFX-mod maximum design value of 2 MA, since in this case local power deposition can be as high as 10 MW m−2. Since the first wall of RFX-mod is entirely covered by graphite tiles different techniques have been tested to control hydrogen wall influx: He glow discharges cleaning, He discharges at high plasma currents, wall boronization and baking. With the best results obtained by boronization, at high plasma currents all such techniques improve the situation but do not allow a complete and stationary hydrogen influx reduction. Furthermore, in the presence of localized high power load the wall still responds providing very high influxes. In order to improve this situation wall conditioning by lithium has been tested. As a first lithization method to deposit a controllable amount of lithium on the wall, a room temperature pellet injector has been used (maximum pellet diameter of 1.8 mm and maximum length of 5 mm). Lithium coatings with a theoretical thickness of about 10 nm have been applied both to clean graphite tiles and over boronized ones. Lithization demonstrated to be effective in lowering hydrogen wall recycling to a value smaller than that of boronized graphite, with the effect lasting 20–30% more than in the boronized case. Compared with boronization, lithization slightly improves (by about 30%) particle confinement time and also clearly affects edge particle transport providing a lower edge density and more peaked density profiles. Lithization also reduces carbon content by about 10% over boronization but still no clear improvement has been observed in terms of energy confinement. Similar results have been obtained performing lithization over boronized graphite.
First Report of Ziziphus jujuba Wilt Caused by Fusarium oxysporum in China
Authors: Gao F. , Xiang Z. , Zhang Y. L.
Published: January 2012

Chinese jujube (Ziziphus jujuba Mill.) is widely planted in Xinjiang Province of China for fruit and as an effective herbal remedy. Wilt symptoms were observed on field-grown Z. jujuba during the spring and fall of 2010 and 2011. Diseased plants exhibited symptoms including wilted leaves, stunted growth, extensive brown discoloration on stems, and eventually death. In severe cases, approximately 60% of the plants in the field died. Repeated isolations from discolored stem vascular tissues were made on potato dextrose agar (PDA) after disinfestation in 1% HgCl2 for 1 min and dipping in 70% ethanol for 10 s. Petri dishes were then incubated in complete darkness at 26°C for 7 days. All colonies on PDA had pale pink-salmon-colored mycelia. Macroconidia were mostly three to five septate, slightly curved, and ranged from 2.9 to 11.9 × 29.5 to 45 μm. Microconidia were abundant, generally single celled, oval to kidney shaped, and ranged from 2.5 to 5 × 7.5 to 11.5 μm in false heads on short monophialides. Chlamydospores were single or in pairs and profusely distributed. These characteristics were similar to those of Fusarium oxysporum (2). The internal transcribed spacer (ITS) rDNA region was amplified with primers ITS1/ITS4 and sequenced (1). BLASTn analysis of the sequence (GenBank Accession No. JQ039331) showed a 99% homology with several isolates of F. oxysporum in the GenBank database. Pathogenicity tests were conducted on healthy, 2-month-old seedlings and 1-month-old rooted cuttings of Z. jujuba under greenhouse conditions. Plants were inoculated with sterilized mixtures of wheat and barley seeds (1:1) that were incubated in a F. oxysporum isolate spore suspension (1 × 107 conidia/ml) at 25°C for 7 to 10 days. The seeds (3 g per plant) were placed around the collar of each healthy plant under the soil surface and incubated at 25 to 28°C in a greenhouse. Control plants were sown in sterile soil without inoculated seeds. In 3 weeks, inoculated plants developed leaf wilt and chlorosis, stunted growth, brown discolored vascular tissue on stems, and finally died, which is similar to that observed in the field. F. oxysporum was reisolated from the stems of diseased plants, confirming Koch's postulates. Control seedlings were symptom free. F. oxysporum has been known to cause wilt disease on cotton and tomato in Xinjiang Province (3). However, to our knowledge, this is the first report of a natural occurrence of Chinese jujube wilt disease on commercial fields caused by F. oxysporum in China.

References: (1) G. M. Arruda et al. Plant Pathol. 54:53, 2005. (2) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Publishing, Ames, IA, 2006. (3) F. X. Tian et al. Acta Phytopathol. Sin. 11:27, 1981.
A review of Bayesian state-space modelling of capture–recapture–recovery data
Authors: King Ruth
Published: January 2012

Traditionally, state-space models are fitted to data where there is uncertainty in the observation or measurement of the system. State-space models are partitioned into an underlying system process describing the transitions of the true states of the system over time and the observation process linking the observations of the system to the true states. Open population capture–recapture–recovery data can be modelled in this framework by regarding the system process as the state of each individual observed within the study in terms of being alive or dead, and the observation process the recapture and/or recovery process. The traditional observation error of a state-space model is incorporated via the recapture/recovery probabilities being less than unity. The models can be fitted using a Bayesian data augmentation approach and in standard BUGS packages. Applying this state-space framework to such data permits additional complexities including individual heterogeneity to be fitted to the data at very little additional programming effort. We consider the efficiency of the state-space model fitting approach by considering a random effects model for capture–recapture data relating to dippers and compare different Bayesian model-fitting algorithms within WinBUGS.
Turtle mating patterns buffer against disruptive effects of climate change
Authors: Wright Lucy I. , Stokes Kimberley L. , Fuller Wayne J. , Godley Brendan J. , McGowan Andrew , Snape Robin , Tregenza Tom , Broderick Annette C.
Published: January 2012

For organisms with temperature-dependent sex determination (TSD), skewed offspring sex ratios are common. However, climate warming poses the unique threat of producing extreme sex ratio biases that could ultimately lead to population extinctions. In marine turtles, highly female-skewed hatchling sex ratios already occur and predicted increases in global temperatures are expected to exacerbate this trend, unless species can adapt. However, it is not known whether offspring sex ratios persist into adulthood, or whether variation in male mating success intensifies the impact of a shortage of males on effective population size. Here, we use parentage analysis to show that in a rookery of the endangered green turtle (
Chelonia mydas
), despite an offspring sex ratio of 95 per cent females, there were at least 1.4 reproductive males to every breeding female. Our results suggest that male reproductive intervals may be shorter than the 2–4 years typical for females, and/or that males move between aggregations of receptive females, an inference supported by our satellite tracking, which shows that male turtles may visit multiple rookeries. We suggest that male mating patterns have the potential to buffer the disruptive effects of climate change on marine turtle populations, many of which are already seriously threatened.
Keeping returns optimal: gain control exerted through sensitivity adjustments in the harbour porpoise auditory system
Authors: Linnenschmidt Meike , Beedholm Kristian , Wahlberg Magnus , Højer-Kristensen Jakob , Nachtigall Paul E.
Published: January 2012

Animals that use echolocation (biosonar) listen to acoustic signals with a large range of intensities, because echo levels vary with the fourth power of the animal's distance to the target. In man-made sonar, engineers apply automatic gain control to stabilize the echo energy levels, thereby rendering them independent of distance to the target. Both toothed whales and bats vary the level of their echolocation clicks to compensate for the distance-related energy loss. By monitoring the auditory brainstem response (ABR) during a psychophysical task, we found that a harbour porpoise (
Phocoena phocoena
), in addition to adjusting the sound level of the outgoing signals up to 5.4 dB, also reduces its ABR threshold by 6 dB when the target distance doubles. This self-induced threshold shift increases the dynamic range of the biosonar system and compensates for half of the variation of energy that is caused by changes in the distance to the target. In combination with an increased source level as a function of target range, this helps the porpoise to maintain a stable echo-evoked ABR amplitude irrespective of target range, and is therefore probably an important tool enabling porpoises to efficiently analyse and classify received echoes.