bluuebunny/crossref_metadata_2025 huggingface dataset:
On Blödite from the Punjab Salt Range
Authors: Mallet F. R.
Published: December 2006

The Salt Range of the Northern Punjab derives its name from the numerous beds of rock salt which are there included amidst the pre-Cambrian strata. Some of these salt beds are of great purity and immense thickness, and have been utilised as a source of the mineral from a remote period, while extensive mines have been opened out by Government since the annexation of the province. The blödite referred to below was discovered in these workings by Dr. H. Warth, lately Deputy Superintendent of the Geological Survey of India, but who, at the time alluded to, held charge of the mines in question.
Augelite from a New Locality in Bolivia
Authors: Spencer L. J.
Published: December 2006

In a recent number of this Magazine (vol XI, 1895, p. 16) augelite was shown to be a definite mineral species, having the chemical composition AlPO4.Al(OH)3, and erystallising in the monosymme{ric system. Owing to its rarity, or perhaps to its similarity in appearance to barytes, it has previously only been described three times in mineralogieal literature, and has been f, mnd at only two localities, namely, Westans in Sweden and Machacamarca in Bolivia. It is therefore of interest to be able to record the mineral from a new locality.
Stanniferous Argyrodite from Bolivia: The Identity of the So-Called “Crystallised Brongniardite” with Argyrodite-Canfieldite
Authors: Prior G. T. , Spencer L. J.
Published: December 2006

The occurrence in Bolivia of minerals containing the rare element germanium has been recently noted by Prof. S. L. Penfield. One of these minerals from Potosi, described bv him in 1893, has the chemical composition of the Freiberg argyrodite (the original source of germanium), but was determined to be cubic, and not monosymmetrie, the system to which argyrodite was originally referred. To the supposed new mineral the name eanfieldite was given, but when Weisbach's reexamination showed that the Freiberg argyrodite was possibly ctlbie, the name was transferred by Penfield to another mineral containing germanium, which he described in 1894.
Atacamite from Sierra Gorda, Chili
Authors: Smith G. F. Herbert
Published: December 2006

In this paper are recorded the observations made upon four exceptionally good specimens of atacamite in the British Museum, which have been submitted to careful study with tile object of determining the geometrical and physical characters of the mineral with greater accuracy than has hitherto been possible. The axial ratios have been calculated with the utmost refinement, an attempt has been made to determine the crystallographic symmetry by a study of the etched figures, and the values of the principal indices of refraction have for the first time been obtained.
On Spharostilbite
Authors: Prior G. T.
Published: December 2006

Sphærostilbite was one of a number of sub-species which Beudant in his Mineralogy, published in 1832, separated from ordinary stilblte owing to slight differences in chemical composition. In a typical specimen from the Faroe Islands he describes the sphmrosfilbite as innplanted upon ordinary stilhite, in the form of small globules, presenting a fibrous radiated structure and brilliant pearly lustre on the fractured surface. Unlike stilhite, it gelatinlsed with acids, and it also had a specific gravity (2.31) slightly higher than that of stilhite. According to the analyses given by Beudant, however, it differed in chemical composition so little from ordinary stilbite that in later text-books (Glocker, 1839; Breithaupt, 1847, &c.) it has always been referred to that species.
On Senaite, a new Mineral belonging to the Ilmenite Group, from Brazil
Authors: Hussak E. , Prior G. T.
Published: December 2006

This new ilmenite-like mineral, containing lead and manganese, was found in rounded fragments and rough crystals in the diamond bearing sands of Diamantina, Minas Geraes, Brazil (at Dattas, Rio Cipó, &c.).
Note on Peculiar Quartz-Pseudomorphs Found at the Owera Mine, Opitonui, North Island, New Zealand
Authors: Ulrich G. H. F.
Published: December 2006

The Owera Mine is opened on a line of lode or reef consisting of small auriferous quartz veins traversing decomposed hyperstheneaugite andesite. The quartz of the veins is highly ferruginous, and full of little patches of brown hæmatite indicating decomposed pre-existing pyrite, remnants of which are occasionally observed. It is in connection with the veins in the soft country rock and near the surface that the pseudomorphs under notice are found, and it seems probable that they owe their origin to infiltration of silica into cavities left by removal of calcite, though none has the actual form of a crystal of that mineral, which, in fact, is quite absent at the place Yet the specimen (No. 2) found with some of the pseudo-crystals tends to support this supposed origin, the hollows and, more clearly, wax impressions of them showing that the removed crystals were scalenohedra.
Plaqionite, Heteromorphite and Semseyite as Members of a Natural Group of Minerals
Authors: Spencer L. J. , Prior G. T.
Published: December 2006

In a recent number of this Magazine (1897, XI. p. 192) a paper by me on "The Crystallography of Plagionite" gives the results of goniometric measurements and specific gravity determinations made on crystals of plagionite from Wolfsberg in the Harz; it was also suggested on crystallographic grounds that the mineral from Arnsberg in Westphalia described by Pisani as heteromorphite was identical with plagionite: but as no quantitative chemical analyses were made on the material measured, these results were not altogether satisfactory.
Riebeckite in Trachytic Rocks from Abyssinia
Authors: Prior G. T.
Published: December 2006

It is now ten years since Sauer first described under the name of riebeckite a new species of blue hornblende in the granite of Socotra.

Since that time its occurrence in the British Isles has been noted in the " felsite " of Mynydd Mawr, N. Wales ; in the " microgranite " of Ailsa Craig, Firth of Clyde; in glacial deposits from the Isle of Man; Moel Tryfaen, N. Wales; Greystones, Co. Wicklow; and Greenore, Carlingford; in granophyre from Meall Dearg, Skye; and in felsite from Middle Eildon, Roxburghshire.
Communications from the Oxford Mineralogical Laboratory. On the constitution of the mineral Arsenates and Phosphates
Authors: Hartley E. G. J.
Published: December 2006

This mineral was originally described as a hydrated copper-arsenate. Analyses of copper-arsenate are given as far back as 1801 by Vauquelin (Journ. des Mines, 1801, X. 562), and by Chenevix in the Philosophical Transactions (for 1801); but at this early date the analyses seem to refer partly to ehalcophyllite and partly to olivenite.
On Langbeinite from the Punjab Salt Range
Authors: Mallet F. R.
Published: December 2006

In the eleventh volume of the Mineralogical Magazine, p. 817, in connection with the occurrence of blödite at the Mayo mines, in the Salt Range, allusion is incidentally made to a potassio-masnesian deposit, which was discovered there by Dr. H. Warth in 1878. It occurred as a lenticular stratum in the ' kallar' (impure rock salt) hand separating the Sujewal and Purwála salt beds. The material was more or less mixed up with the ' kallar' itself, and the deposit appeared to be of very limited extent.
On the Cliftonite and Tanite of the Meteoric Iron found in 1884 in the Sub-district of Youndegin, Western Australia
Authors: Fletcher L.
Published: December 2006

In a previous paper, published in 1887, the author described some remarkable crystals of graphitic carbon (Cliftonite) obtained from the meteoric iron of Youndegin, Western Australia; the isolated material weighed only 3 milligrams, and had been left as an insoluble residue after the treatment of 8.32 grams of the iron with aqua regia.
A Three-Circle Goniometer
Authors: Herbert Smith G. F.
Published: December 2006

The object of goniometrical measurement is to determine in the simplest and quickest manner possible the geometrical constants of crystals and the indices of their faces. The ideal instrument should enable the observations to he conveniently and quickly made, and present them in such a form that the indices of the faces may be easily calculated. It is claimed for the tbrm of goniometer described in this paper that it does approximate to such an instrument. Before entering into the description it will not be out of place to discuss briefly the two types at present in existence, and point out their advantages and disadvantages.
On the Meteoric Stones which fell near Zomba, British Central Africa, on January 25th, 1899: with notes on the chemical analysis of such bodies. [With a map of the District, plate I.]
Authors: Fletcher L.
Published: December 2006

On January 25th, 1899, at 7.54 a.m., a loud noise as of an explosion was heard at the settlement of Zomba, British Central Africa, and for many miles around ; almost simultaneously therewith, several small stones were seen to reach the earth in the neighbourhood of Zomba and were collected by the observers of their fall.

Mr. Alfred Sharpe, C.B., His Majesty's Commissioner and Consul. General for the Protectorate of British Central Africa, Mr. J. F. Cunningham, Secretary to the Administration, and Mr. J. McClounie, the Acting Collector of Revenues, on hearing the detonation, surmised that it had an origin in the entry of a meteorite into the earth's atmosphere, and with praiseworthy zeal and energy at once proceeded to collect, by aid of the telegraph and by personal interviews with the witnesses, all the reliable evidence that could be obtained relative to so extraordinary a phenomenon.
Marshite, Miersite, and Iodyrite from Broken Hill, New South Wales
Authors: Spencer L. J.
Published: December 2006

Minerals containing iodine as an essential constituent are of rare occurrence in nature. The most common, and that first described, is silver iodide, which was analysed by Vauquelin in 1825; hexagonal crystals of iodyrite were described by Des Cloizeaux in 1854. Other iodides are marshite and the new mineral miersite ; iodobromite and schwartzembergite also contain considerable amounts of iodine. The existence of mercury iodide seems to be doubtful; the supposed mercury iodide from Broken Hill consists of an intimate mixture of cinnabar and iodyrite. Two iodates are also known, namely lautarite and dietzeite.
Addition to a former note on the rotation of points and planes about an axis
Authors: Hudson R. W. H. T.
Published: December 2006

The evaluation of the determinant

occurriug at the foot of page 345, Vol. XII, can be effected without first squaring it. Multiply Δ1 by

say D1/2, which is the value of the determinant

The result is

Similarly Δ2 and Δ3 may be evaluated.
Note on a British occurrence of Mirabilite
Authors: Trechmann C. O.
Published: December 2006

In August, 1900, several specimens of this mineral were found attached to gypsum-rock supplied to me from the quarry at Kirkby There, in Westmoreland, by Messrs. Joseph Robinson & Co., Ld., of Carlisle, who kindly inform me that the bed of this rock is about 20 feet thick, being overlaid by about 22 feet of marl, &c. There is very little anhydrite, not more than 2 or 3 inches, which, as a rule, is found in the middle of the bed of gypsum. Although I have used this rock for commercial purposes for years past in regular quantities, yet the mirabilite was never previously noticed.
On an occurrence of Minerals at Haddam Neck, Connecticut, U.S.A. (With Plate IV.)
Authors: Bowman H. L.
Published: December 2006

In the summer of 1896 the Oxford Museum was enriched by a fine series of about eighty mineral specimens from a newly opened quarry at Haddam Neck in Connecticut, which were kindly presented by Mr. Ernest Schernikow of New York.

The species included in the series are green and pink tourmaline, albite, microcline, green and pink apatite, brown fluor, beryl, quartz, cookeite, lilac lepidolite, greenish-white muscovite, and a peculiar pink fibrous variety of the same mineral. To these must also be added, as occurring at the same place, green fluor, microlite, and columbite.

The locality is described as Haddam Neck, a village opposite to Haddam, on the other (eastern) bank of the Connecticut River, which is here about half a mile wide.
Mineralogical notes on Western Australian Tellurides: the non-existence of ‘Kalgoorlite’ and ‘Coolgardite’ as mineral species
Authors: Spencer L. J.
Published: December 2006

Since the occurrence of tellurides of gold in Western Australia was first recognized by Mr. Arthur G. Holroyd in May, 1896, these minerals have proved to be of the greatest importance as a source of gold; and in fact the telluride mines at Kalgoorlie in the East Coolgardie gold-field now yield as much gold as all the remaining gold-fields of Western Australia taken together.

Although the occurrence of traces of telluride of gold has been reported from one or two other localities in the neighbouring portions of Western Australia, it is only in a quite small area around Kalgoorlie that the tellurides are mined. Here they occur as lodes, or rather as large lenticular masses and as impregnations, in schistose rocks.
On some new forms prominently developed on crystals of Proustite
Authors: Lamplough F. E. E.
Published: December 2006

Whilst determining some crystals of proustite in the Mineralogical Museum at Cambridge, and which came from Bolivia or some other part of South America, my attention was attracted by faces of trigonal pyramids, which, as shown in figs. 1 and 2, are the most conspicuous on the crystals. On measurement, these faces were found to correspond very nearly to those of the rhombohedra {73̄3̄} = 10 R (fig. 1) and {94̄4̄} = 13R (fig. 2). The figures represent with fair accuracy the relatively large development of the faces of these new forms. Another form, {11.7̄.7̄} = –6 R, represented by a single face on the lower end of one crystal, is also new for proustite.
Crystalline forms of Carbides and Silicides of Iron and Manganese (‘Ferro-manganese,’ &c.).
Authors: Spencer L. J.
Published: December 2006

Mallard in 1879, noted that crystals of the metallurgical products ‘Spiegeleisen’ and ‘ferro-manganese’ are of two kinds. Both show a prism-zone of six faces, but when the percentage of manganese reaches a certain amount there is an abrupt change in the habit of the crystals and in the angles between their faces. Crystals containing from 11 up to 52 or 55 per cent. of manganese are lamellar, and were found to have a prism-angle (mm′′′ = 110 : 11̄) of 6° 27′, while crystals containing a larger amount of manganese are acicular and have a pseudo-hexagonal prism-zone, the angular measurements of which varied between 58° 42′ and 61° 20′.
On Teallite, a new sulphostannite of lead from Bolivia ; and its relations to Franckeite and Cylindrite
Authors: Prior G. T.
Published: December 2006

Amongst the specimens recently selected for the British Museum from the collection of South American minerals brought together by the late Theodor Hohmann, are two on which occurs a mineral in thin laminae resembling graphite. From the locality and associations, the mineral was at first presumed to be either franckeite or cylindrite, the two sulphantimonite-sulphostannates of lead from Bolivia, which were described in 1893 by Stelzner and Frenzel respectively. Qualitative analysis, however, soon showed that, although similar to them in physical characters, it differed chemically from both franckeite and cylindrite in containing no antimony, but only lead, tin, and sulphur.

Of the two specimens from the Hohmann collection, one was labelled ‘sulphoselenide of lead from Bolivia,’ and the other ‘selenide of lead from Atacama,’ so that unfortunately the precise locality of the mineral is at present unknown. In all probability both specimens came from the same district in Bolivla, since in appearance they are very similar.
A new device for separating minerals by means of heavy liquids
Authors: Hartley Harold
Published: December 2006

During the investigation of a zeolite it became necessary to separate small quantities of zeolitic material from a mixture of calcite and other heavier minerals; this could be done most easily by using a liquid of such density that the zeolite just floated, while all the other minerals sank to the bottom. A solution of potassium-mercuric iodide could not be used, as this reacts chemically with zeolites and alters their composition ; acetylene tetrabromide diluted with benzene was therefore chosen, and in consequence the apparatus had to be made entirely of glass. Certain dittlculties were found in using the ordinary form of glass separating apparatus, and to overcome these the form here described was devised.
On an Epidote from Inverness-shire
Authors: Thomas H. H.
Published: December 2006

The mineral to be described was found by Mr. C. T. Clough, M.A., of the Geological Survey, near the junction of the two large streams in Coire Dhorrcail, near Barrisdale on the south side of Loch Hourn, Inverness-shire.

Mr. Clough furnishes me with the following description of the mode of occurrence of the mineral :—

‘The crystals were obtained from a band, which, although its sides are not well exposed, seems to form a nearly horizontal vein-like mass. This band crosses both the bedding and the foliation planes of the muscovite-biotite-gneiss in which it occurs, and which occupies a large area near Barrisdale and Ladhar Bheinn.
On the crystallization of sodium nitrate
Authors: Miets H. A. , Chevalier Jacques
Published: December 2006

Experiments made by Professor Miers and Miss F. Isaac have shown how, by measurements of the refractive index, it is possible to determine for a supersaturated solution the temperature at which it passes from the metastable condition, in which it can only crystallize by inoculation with a crystal of the salt (or of a substance isomorphous with it), to the labile condition, in which it may (and often does) crystallize spontaneously. In a diagram in which concentrations are taken as ordinates and temperatures a abscissae the solubility curve represents the limit between the unsaturated and the metastable state; and the limit between the metastable and the labile state is represented by a similar curve, to which they have given the name ‘Supersolubility curve’.
Gnomonic Projections on two planes
Authors: Evans John W.
Published: December 2006

The gnomonic projection in which the faces of crystals are represented by the points where their normals through a fixed point–the centre of projection–meet a plane–the plane of projection–is already widely used by crystallographers. I propose in the following pages to show the advantages of the simultaneous use of two such planes of projection.

It is in most cases convenient for the two planes to be at right angles, and for the centre of projection to be at an equal (unit) distance from each. Circumstances, however, in some cases render it desirable to vary these conditions. When the planes are at right angles, one may conveniently be described as the horizontal plane, and the other as the vertical plane.
Determination of the optic axial angle of biaxial crystals in parallel polarized light
Authors: Evans John W.
Published: December 2006

It will in the first place be assumed for the sake of simplicity that the crystal to be investigated is immersed in a liquid having a refractive index as nearly as possible equal to the intermediate refractive index (β), so that light travelling along the optic axis t is not appreciably refracted on entering or leaving the crystal.

The observation is made in parallel ight between crossed nicols, which are rotated together till a position of extinction is reached, when the directions of vibration of the nicols wilI be parallel to those in the crystal. If the latter be now rotated on an axis parallel to one of these directions, it will in general show light throughout the revolution, except in the original position and that opposite to it. Occasionally, however, it will remain dark throughout; in that case the axis of rotation is the bisectrix of an optic axial angle.
Note on ‘Feather-ore’ : identity of ‘Domingite’ (=‘Warrenite’) with Jamesonite
Authors: Spencer L. J.
Published: December 2006

The formula 2PbS. Sb2S3, given for jamesonite in all the textbooks, does not belong to jamesonite at all, but to the ‘Federerz’ (‘feather-ore’) from Wolfsherg in the Harz analysed by H. Rose in 1829, and for which the mineralogical names wolfsberglte (Huot, 1841) and plumosite (Haidinger, 1845) have been proposed. Rose's formula for the cleavable jamesonite from Cornwall was 3PbS. 2Sb2S3. In 1860 Rammelsberg united these, together with heteromorphite, under the name jamesonite and with the formula 2PbS. Sb2S3 a : this has since been followed in the textbooks, but, as will be pointed out below, it is very probable that there are here three distinct mineral species.
Notes on skiodroms and isogyres
Authors: Evans John W.
Published: December 2006

Professor Becke's paper on skiodroms marks an important advance in our knowledge of the shadows, or isogyres, which are seen when sections of crystals are examined in convergent polarized light. The isogyres can also be advantageously studied in mineral grains, where the irregular shape disturbs the distribution of the interference colours, but has much less effect on the shadows due to the coincidence of directions of vibration in the crystal with those of one of the nicols.
Ilmenite from Jacupiranga, Brazil
Authors: Herbert Smith G. F.
Published: December 2006

During the summer of this year certain crystals of zirkelite from Ceylon were entrusted to the author for crystallographical investigation, and in that connexion the specimens placed under this species in the British Museum collection were examined for the sake of comparison. The whole of the latter specimens come from Jaeupiranga in São Paulo, Brazil: some of them had been presented by Dr. E. Hussak and formed part of the material on which he and Dr. G. T. Prior conducted their investigation which led to the first discovery of zirkelite, while the remainder were purchased subsequently. The latter included a lot of small, brilliant crystals (numbered 86034 in the General Register) which differed so markedly in lustre from the other crystals as to suggest that they had been incorrectly determined.
Notes on some Bolivian minerals (Jamesonite, Andorite, Cassiterite, Tourmaline, &c.)
Authors: Spencer L. J.
Published: December 2006

During the last twelve years I have communicated to this Society, often in collaboration with Dr. G. T. Prior, several papers descriptive of Bolivian minerals. These papers have dealt primarily with the species augelite, andorite, argyrodite, stannite, and chaleostibite, though many others have been examined and in some cases incidentally mentioned. The latter, as being of lesser general interest, or as not having led to sufficiently important results for separate publication, are now collected together in the present notes.
Cassiterite pseudomorphs from Bolivia
Authors: Pearce Richard
Published: December 2006

One of the peculiarities of Bolivian tin-ores is the frequent occurrence of cindery and cellular masses of cassiterite, which is presumably of secondary origin. But, apart from impressions of quartz crystals, definite crystal-forms are rarely shown by this pseudomorphous cassiterite.

The pseudomorphs to be now described are from the Tres Cruces district, and were collected by my son, Mr. A. W. Pearce. The crystallographic determinations have been made by Mr. L. J. Spencer, and the specimens examined by him have been presented to the British Museum. The material consists of cavernous masses of dark brown, finely crystalline and granular cassiterite, associated with which is a pale yellow, ochreous substance.
A new model of Refractometer
Authors: Herbert Smith G. F.
Published: December 2006

The instrument described in this paper is identical in principle with the small refractometer designed by the author more than three years ago, but differs from it in several details which are of considerable practical importance. As in the earlier form, a compensative lens is introduced of such curvature and focal length that the focal surface of the optical combination is a plane within the range for which the instrument is required, and consequently the critical edges are sharply defined in monochromatic light for all positions. It will be more convenient, before entering into the description, to take the features which have been changed.
On the occurrence of silver ore in the Perran mine, Perran Uthnoe, Cornwall
Authors: Butler Francis H.
Published: December 2006

The deposit known as the Wheal Sedgman lode is inclined to the west a few degrees from the vertical, and runs in a direction about 10° W. of N. (magnetic) through the parish of Perran Uthnoe, near Marazion, Cornwall. In its course seawards from the approximately E. and W. lode formerly worked in the Great Wheal Neptune mine, it traverses the North and South Trebarvah tin and copper lodes. It is crossed by the shore-line on Perran Sands, about 500 yards to the west of Trevean cliff. Between that spot and Cuddan Point, to the S.E., where it is again laid bare, it has been superficially removed by marine denudation. The numerous N. and S. diabase dikes of the district show in placts much disseminated pyrrhotite, and one of them runs nearly parallel to the east side, or foot wall, of the Sedgman lode.
The question of a relation between the Parallel Growths of Crystals and Isomorphous Miscibility, and the bearing of Parallel Growths on questions of Isomorphism
Authors: Barker Thomas Vipond
Published: December 2006

One of the most important and striking properties of isomorphous substances is their capacity for forming microscopically homogeneous mixed crystals, the physical properties of which are, as Retgers has especially shown, intermediate between the properties of the constituents. With the great majority of isomorphous substances the mixed crystals can be obtained in all proportions, but with others the miscibility is limited.

The first case of restricted miscibility was discovered by Retgers in potassium phosphate (mol. vo1.=58.25) and ammonium phosphate (64.17) crystallizing in the tetragonal system ; he did not determine the exact proportions which each salt can take up of the other, but estimated them to be about 20 per cent. each way.
On Strüverite and its relation to Ilmenorutile
Authors: Prior G. T. , Zambonini F.
Published: December 2006

The mineral strüverite occurs as a rare accessory constituent of the pegmatite which is found in large detrital masses in the neighbourhood of Craveggia (Val Vigezzo, northern Piedmont), namely on the Piano dei Lavonchi and in other localities on the eastern slope of the mountain across which runs the road from Vasca to the Alp Marco. In this pegmatite Professor G. Spezia in 1882 noted the occurrence of beryl, and two years later Professor G. Strüver that of columbite, a mineral which had not hitherto been found in the Alps. Still later, notices of other rare minerals from the pegmatiie were published by Professor A. Piccini and Professor A. Cossa.
On the structure of Perovskite from the Burgumer Alp, Pfitschthal, Tyrol
Authors: Bowman H. L.
Published: December 2006

The question of the system to which perovskite should be referred, and the explanation of the discrepancy between its form and optical-properties, have been the subject of much discussion among crystallograpbers ever since the discovery by Des Cloizeaux, in 1858, of the double refraction of crystals of calciam titanate from Zermatt, having the same composition as the crystals of cubic form from the Ural Mountains, to which the name perovskite had been given by G. Rose in 1889.
The electrostatic separation of minerals
Authors: Crook T.
Published: December 2006

When a mineral fragment is brought under the influence of an electrostatic charge, its behaviour depends chiefly upon the conductivity of the mineral and that of the surface on which it is lying. This fact can be effectively demonstrated by placing fragments of amber (sp. gr. about 1.1) and pyrite (sp. gr. about 5) on a metallic surface, such as that of a copper plate, and noting their behaviour when a rod of vulcanite, which has been electrified by rubbing with cat's skin, is brought near them. Under these conditions a small fragment of dry amber, weighing not more than one milligram, is not attracted to the rubbed rod, although the rod be brought almost in contact with it; whilst a large piece of pyrite weighing as much as 150 milligrams jumps visibly from the plate with the rod held at some distance from it.
On the occurrence of Gyrolite in County Antrim
Authors: Fleischmann F. N. A.
Published: December 2006

Although the mineral gyrolite has long been known to occur in the British Isles, namely in the basalt lavas of Skye, Mull, and the Treshnish Islands, &c., off the west coast of Scotland, and has more recently been described from the cliffs between Ardtornish Bay and the fault of Dearg Allt in Argyllshire on the mainland, no instance of its occurrence in the lavas of the north of Ireland has hitherto been recorded.

The examination, however, of a large number of specimens collected both for me and by myself during the past year and a half has shown that the mineral, though occurring in small quantity relative to the other zeolites with which it is associated, is fairly widely distributed throughout the harder lavas in the neighbourhood of Belfast.
Analyses of Seligmannite, zinciferous Tennantite (‘Binnite’), and Fuchsite from the Lengenbach quarry, Binnenthal
Authors: Prior G. T.
Published: December 2006

The crystallographic and other physical characters of seligmannite from the well-known quarry in the Lengenbach, Binnenthal, were first described by Professor Baumhauer in 1901. In its crystallographic characters the mineral was found to be closely allied to bournonite, which it resembled in the habit of the crystals and the repeated twinning on the prism-planes.
Axes of symmetry and the crystallographic classes
Authors: Evans John W.
Published: December 2006

It is usual to divide axes of rotatory symmetry into those of the first and those of the second sort. In the former a crystal is brought into coincidence by a rotation through a certain angle round the axis and in the latter by such a rotation followed by a reflection about (or, as I prefer to say, a reversal relatively to) the plane at right angles to the axis. In 1906 Mr. H. Hilton proposed to define an axis of rotatory symmetry of the second sort as one in which the rotation was followed by an inversion about (reversal relatively to) a point, and he showed that his proposal would, if adopted, simplify the definition of the crystallographic classes.
Selective targeting of the LIGHT-HVEM costimulatory system for the treatment of graft-versus-host disease
Authors: Xu Yanhui , Flies Andrew S. , Flies Dallas B. , Zhu Gefeng , Anand Sudarshan , Flies Sarah J. , Xu Haiying , Anders Robert A. , Hancock Wayne W. , Chen Lieping , Tamada Koji
Published: December 2006

Decoy lymphotoxin β receptor (LTβR) has potent immune inhibitory activities and thus represents a promising biologic for the treatment of inflammation, autoimmune diseases, and graft-versus-host disease (GVHD). As this reagent interrupts multiple molecular interactions, including LTβ-LTβR and LIGHT-HVEM/LTβR, underlying molecular mechanisms have yet to be fully understood. In this study, we demonstrate that blockade of the LIGHT-HVEM pathway is sufficient to induce amelioration of GVHD in mouse models. Anti–host cytotoxic T lymphocyte (CTL) activity following in vivo transfer of allogeneic lymphocytes was completely abrogated when LIGHT- or HVEM-deficient (KO) T cells were used as donor cells. Accordingly, survival of the recipient mice following the transfer of allogeneic bone marrow cells plus LIGHT-KO or HVEM-KO T cells was significantly prolonged. In the absence of LIGHT-HVEM costimulation, alloreactive donor T cells undergo vigorous apoptosis while their proliferative potential remains intact. Furthermore, we prepared a neutralizing monoclonal antibody (mAb) specific to HVEM and showed that administration of anti–HVEM mAb profoundly ameliorated GVHD and led to complete hematopoietic chimerism with donor cells. Collectively, our results demonstrate an indispensable role of LIGHT-HVEM costimulation in the pathogenesis of GVHD and illustrate a novel target for selective immunotherapy in allogeneic bone marrow transplantation.
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
Authors: Sartor Maureen A , Tomlinson Craig R , Wesselkamper Scott C , Sivaganesan Siva , Leikauf George D , Medvedovic Mario
Published: December 2006

Background

The small sample sizes often used for microarray experiments result in poor estimates of variance if each gene is considered independently. Yet accurately estimating variability of gene expression measurements in microarray experiments is essential for correctly identifying differentially expressed genes. Several recently developed methods for testing differential expression of genes utilize hierarchical Bayesian models to "pool" information from multiple genes. We have developed a statistical testing procedure that further improves upon current methods by incorporating the well-documented relationship between the absolute gene expression level and the variance of gene expression measurements into the general empirical Bayes framework.

Results

We present a novel Bayesian moderated-T, which we show to perform favorably in simulations, with two real, dual-channel microarray experiments and in two controlled single-channel experiments. In simulations, the new method achieved greater power while correctly estimating the true proportion of false positives, and in the analysis of two publicly-available "spike-in" experiments, the new method performed favorably compared to all tested alternatives. We also applied our method to two experimental datasets and discuss the additional biological insights as revealed by our method in contrast to the others. The R-source code for implementing our algorithm is freely available athttp://eh3.uc.edu/ibmt.

Conclusion

We use a Bayesian hierarchical normal model to define a novel Intensity-Based Moderated T-statistic (IBMT). The method is completely data-dependent using empirical Bayes philosophy to estimate hyperparameters, and thus does not require specification of any free parameters. IBMT has the strength of balancing two important factors in the analysis of microarray data: the degree of independence of variances relative to the degree of identity (i.e.t-tests vs. equal variance assumption), and the relationship between variance and signal intensity. When this variance-intensity relationship is weak or does not exist, IBMT reduces to a previously described moderated t-statistic. Furthermore, our method may be directly applied to any array platform and experimental design. Together, these properties show IBMT to be a valuable option in the analysis of virtually any microarray experiment.
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition
Authors: Tsai Richard Tzong-Han , Sung Cheng-Lung , Dai Hong-Jie , Hung Hsieh-Chuan , Sung Ting-Yi , Hsu Wen-Lian
Published: December 2006

Background

Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. They have many irregularities and sometimes appear in ambiguous contexts. In recent years, machine-learning (ML) approaches have become increasingly common and now represent the cutting edge of Bio-NER technology. This paper addresses three problems faced by ML-based Bio-NER systems. First, most ML approaches usually employ singleton features that comprise one linguistic property (e.g., the current word is capitalized) and at least one class tag (e.g., B-protein, the beginning of a protein name). However, such features may be insufficient in cases where multiple properties must be considered. Adding conjunction features that contain multiple properties can be beneficial, but it would be infeasible to include all conjunction features in an NER model since memory resources are limited and some features are ineffective. To resolve the problem, we use a sequential forward search algorithm to select an effective set of features. Second, variations in the numerical parts of biomedical terms (e.g., "2" in the biomedical term IL2) cause data sparseness and generate many redundant features. In this case, we apply numerical normalization, which solves the problem by replacing all numerals in a term with one representative numeral to help classify named entities. Third, the assignment of NE tags does not depend solely on the target word's closest neighbors, but may depend on words outside the context window (e.g., a context window of five consists of the current word plus two preceding and two subsequent words). We use global patterns generated by the Smith-Waterman local alignment algorithm to identify such structures and modify the results of our ML-based tagger. This is called pattern-based post-processing.

Results

To develop our ML-based Bio-NER system, we employ conditional random fields, which have performed effectively in several well-known tasks, as our underlying ML model. Adding selected conjunction features, applying numerical normalization, and employing pattern-based post-processing improve the F-scores by 1.67%, 1.04%, and 0.57%, respectively. The combined increase of 3.28% yields a total score of 72.98%, which is better than the baseline system that only uses singleton features.

Conclusion

We demonstrate the benefits of using the sequential forward search algorithm to select effective conjunction feature groups. In addition, we show that numerical normalization can effectively reduce the number of redundant and unseen features. Furthermore, the Smith-Waterman local alignment algorithm can help ML-based Bio-NER deal with difficult cases that need longer context windows.
Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
Authors: Lin HH , Han LY , Zhang HL , Zheng CJ , Xie B , Cao ZW , Chen YZ
Published: December 2006

Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diversity, it is desirable to explore additional methods for predicting metal-binding proteins irrespective of sequence similarity. This work explores support vector machines (SVM) as such a method. SVM prediction systems were developed by using 53,333 metal-binding and 147,347 non-metal-binding proteins, and evaluated by an independent set of 31,448 metal-binding and 79,051 non-metal-binding proteins. The computed prediction accuracy is 86.3%, 81.6%, 83.5%, 94.0%, 81.2%, 85.4%, 77.6%, 90.4%, 90.9%, 74.9% and 78.1% for calcium-binding, cobalt-binding, copper-binding, iron-binding, magnesium-binding, manganese-binding, nickel-binding, potassium-binding, sodium-binding, zinc-binding, and all metal-binding proteins respectively. The accuracy for the non-member proteins of each class is 88.2%, 99.9%, 98.1%, 91.4%, 87.9%, 94.5%, 99.2%, 99.9%, 99.9%, 98.0%, and 88.0% respectively. Comparable accuracies were obtained by using a different SVM kernel function. Our method predicts 67% of the 87 metal-binding proteins non-homologous to any protein in the Swissprot database and 85.3% of the 333 proteins of known metal-binding domains as metal-binding. These suggest the usefulness of SVM for facilitating the prediction of metal-binding proteins. Our software can be accessed at the SVMProt server http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi.
SVM-based prediction of caspase substrate cleavage sites
Authors: Wee Lawrence JK , Tan Tin Wee , Ranganathan Shoba
Published: December 2006

Background

Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. Recently, different computational methods have been developed to predict the cleavage sites of caspase substrates with varying degrees of success. As the support vector machines (SVM) algorithm has been shown to be useful in several biological classification problems, we have implemented an SVM-based method to investigate its applicability to this domain.

Results

A set of unique caspase substrates cleavage sites were obtained from literature and used for evaluating the SVM method. Datasets containing (i) the tetrapeptide cleavage sites, (ii) the tetrapeptide cleavage sites, augmented by two adjacent residues, P1' and P2' amino acids and (iii) the tetrapeptide cleavage sites with ten additional upstream and downstream flanking sequences (where available) were tested. The SVM method achieved an accuracy ranging from 81.25% to 97.92% on independent test sets. The SVM method successfully predicted the cleavage of a novel caspase substrate and its mutants.

Conclusion

This study presents an SVM approach for predicting caspase substrate cleavage sites based on the cleavage sites and the downstream and upstream flanking sequences. The method shows an improvement over existing methods and may be useful for predicting hitherto undiscovered cleavage sites.
An evaluation of human protein-protein interaction data in the public domain
Authors: Mathivanan Suresh , Periaswamy Balamurugan , Gandhi TKB , Kandasamy Kumaran , Suresh Shubha , Mohmood Riaz , Ramachandra YL , Pandey Akhilesh
Published: December 2006

Background

Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently available. Each of these databases has their own unique features with a large variation in the type and depth of their annotations.

Results

We analyzed the major publicly available primary databases that contain literature curated PPI information for human proteins. This included BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome databases. The number of binary non-redundant human PPIs ranged from 101 in PDZBase and 346 in MIPS to 11,367 in MINT and 36,617 in HPRD. The number of genes annotated with at least one interactor was 9,427 in HPRD, 4,975 in MINT, 4,614 in IntAct, 3,887 in BIND and <1,000 in the remaining databases. The number of literature citations for the PPIs included in the databases was 43,634 in HPRD, 11,480 in MINT, 10,331 in IntAct, 8,020 in BIND and <2,100 in the remaining databases.

Conclusion

Given the importance of PPIs, we suggest that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date. We hope that our analysis will help guide biomedical scientists in selecting the most appropriate database for their needs especially in light of the dramatic differences in their content.
Evaluation and comparison of mammalian subcellular localization prediction methods
Authors: Sprenger Josefine , Fink J Lynn , Teasdale Rohan D
Published: December 2006

Background

Determination of the subcellular location of a protein is essential to understanding its biochemical function. This information can provide insight into the function of hypothetical or novel proteins. These data are difficult to obtain experimentally but have become especially important since many whole genome sequencing projects have been finished and many resulting protein sequences are still lacking detailed functional information. In order to address this paucity of data, many computational prediction methods have been developed. However, these methods have varying levels of accuracy and perform differently based on the sequences that are presented to the underlying algorithm. It is therefore useful to compare these methods and monitor their performance.

Results

In order to perform a comprehensive survey of prediction methods, we selected only methods that accepted large batches of protein sequences, were publicly available, and were able to predict localization to at least nine of the major subcellular locations (nucleus, cytosol, mitochondrion, extracellular region, plasma membrane, Golgi apparatus, endoplasmic reticulum (ER), peroxisome, and lysosome). The selected methods were CELLO, MultiLoc, Proteome Analyst, pTarget and WoLF PSORT. These methods were evaluated using 3763 mouse proteins from SwissProt that represent the source of the training sets used in development of the individual methods. In addition, an independent evaluation set of 2145 mouse proteins from LOCATE with a bias towards the subcellular localization underrepresented in SwissProt was used. The sensitivity and specificity were calculated for each method and compared to a theoretical value based on what might be observed by random chance.

Conclusion

No individual method had a sufficient level of sensitivity across both evaluation sets that would enable reliable application to hypothetical proteins. All methods showed lower performance on the LOCATE dataset and variable performance on individual subcellular localizations was observed. Proteins localized to the secretory pathway were the most difficult to predict, while nuclear and extracellular proteins were predicted with the highest sensitivity.
Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris
Authors: Tong Joo Chuan , Tan Tin Wee , Sinha Animesh A , Ranganathan Shoba
Published: December 2006

Background

Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The target antigen of PV, desmoglein 3 (Dsg3), is crucial for initiating T-cell response in early disease. Although a number of T-cell specificities within Dsg3 have been reported, the number is limited and the role of T-cells in the pathogenesis of PV remains poorly understood. We report here a structure-based model for the prediction of peptide binding to DRB1*0402 and DQB1*0503. The scoring functions were rigorously trained, tested and validated using experimentally verified peptide sequences.

Results

High predictivity is obtained for both DRB1*0402 (r2= 0.90,s= 1.20 kJ/mol,q2= 0.82,spress= 1.61 kJ/mol) and DQB1*0503 (r2= 0.95,s= 1.20 kJ/mol,q2= 0.75,spress= 2.15 kJ/mol) models, compared to experimental data. We investigated the binding patterns of Dsg3 peptides and illustrate the existence of multiple immunodominant epitopes that may be responsible for both disease initiation and propagation in PV. Further analysis reveals that DRB1*0402 and DQB1*0503 may share similar specificities by binding peptides at different binding registers, thus providing a molecular mechanism for the dual HLA association observed in PV.

Conclusion

Collectively, the results of this study provide interesting new insights into the pathology of PV. This is the first report illustrating high-level of cross-reactivity between both PV-implicated alleles, DRB1*0402 and DQB1*0503, as well as the existence of a potentially large number of T-cell epitopes throughout the entire Dsg3 extracellular domain (ECD) and transmembrane region. Our results reveal that DR4 and DR6 PV may initiate in the ECD and transmembrane region respectively, with implications for immunotherapeutic strategies for the treatment of this autoimmune disease.