Raman and infrared spectroscopic study of kamphaugite-(Y)

We have studied the carbonate mineral kamphaugite-(Y)(CaY(CO3)2(OH)·H2O), a mineral which contains yttrium and specific rare earth elements. Chemical analysis shows the presence of Ca, Y and C. Back scattering SEM appears to indicate a single pure phase. The vibrational spectroscopy of kamphaugite-(Y) was obtained using a combination of Raman and infrared spectroscopy. Two distinct Raman bands observed at 1078 and 1088cm(-1) provide evidence for the non-equivalence of the carbonate anion in the kamphaugite-(Y) structure. Such a concept is supported by the number of bands assigned to the carbonate antisymmetric stretching mode. Multiple bands in the ν4 region offers further support for the non-equivalence of carbonate anions in the structure. Vibrational spectroscopy enables aspects of the structure of the mineral kamphaugite-(Y) to be assessed.

The molecular structure of the borate mineral szaibelyite MgBO2(OH): A vibrational spectroscopic study

We have studied the borate mineral szaibelyite MgBO2(OH) using electron microscopy and vibrational spectroscopy. EDS spectra show a phase composed of Mg with minor amounts of Fe. Both tetrahedral and trigonal boron units are observed. The nominal resolution of the Raman spectrometer is of the order of 2 cm−1 and as such is sufficient enough to identify separate bands for the stretching bands of the two boron isotopes. The Raman band at 1099 cm−1 with a shoulder band at 1093 cm−1 is assigned to BO stretching vibration. Raman bands at 1144, 1157, 1229, 1318 cm−1 are attributed to the BOH in-plane bending modes. Raman bands at 836 and 988 cm−1 are attributed to the antisymmetric stretching modes of tetrahedral boron. The infrared bands at 3559 and 3547 cm−1 are assigned to hydroxyl stretching vibrations. Broad infrared bands at 3269 and 3398 cm−1 are assigned to water stretching vibrations. Infrared bands at 1306, 1352, 1391, 1437 cm−1 are assigned to the antisymmetric stretching vibrations of trigonal boron. Vibrational spectroscopy enables aspects of the molecular structure of the borate mineral szaibelyite to be assessed.

Fine-mapping of the HNF1B multicancer locus identifies candidate variants that mediate endometrial cancer risk

Common variants in the hepatocyte nuclear factor 1 homeobox B (HNF1B) gene are associated with the risk of Type II diabetes and multiple cancers. Evidence to date indicates that cancer risk may be mediated via genetic or epigenetic effects on HNF1B gene expression. We previously found single-nucleotide polymorphisms (SNPs) at the HNF1B locus to be associated with endometrial cancer, and now report extensive fine-mapping and in silico and laboratory analyses of this locus. Analysis of 1184 genotyped and imputed SNPs in 6608 Caucasian cases and 37 925 controls, and 895 Asian cases and 1968 controls, revealed the best signal of association for SNP rs11263763 (P = 8.4 × 10−14, odds ratio = 0.86, 95% confidence interval = 0.82–0.89), located within HNF1B intron 1. Haplotype analysis and conditional analyses provide no evidence of further independent endometrial cancer risk variants at this locus. SNP rs11263763 genotype was associated with HNF1B mRNA expression but not with HNF1B methylation in endometrial tumor samples from The Cancer Genome Atlas. Genetic analyses prioritized rs11263763 and four other SNPs in high-to-moderate linkage disequilibrium as the most likely causal SNPs. Three of these SNPs map to the extended HNF1B promoter based on chromatin marks extending from the minimal promoter region. Reporter assays demonstrated that this extended region reduces activity in combination with the minimal HNF1B promoter, and that the minor alleles of rs11263763 or rs8064454 are associated with decreased HNF1B promoter activity. Our findings provide evidence for a single signal associated with endometrial cancer risk at the HNF1B locus, and that risk is likely mediated via altered HNF1B gene expression.

A SEM, EDS and vibrational spectroscopic study of the clay mineral fraipontite

The mineral fraipontite has been studied by using a combination of scanning electron microscopy with energy dispersive analysis and vibrational spectroscopy (infrared and Raman). Fraipontite is a member of the 1:1 clay minerals of the kaolinite-serpentine group. The mineral contains Zn and Cu and is of formula (Cu,Zn,Al)3(Si,Al)2O5(OH)4. Qualitative chemical analysis of fraipontite shows an aluminium silicate mineral with amounts of Cu and Zn. This kaolinite type mineral has been characterised by Raman and infrared spectroscopy; in this way aspects about the molecular structure of fraipontite clay are elucidated.

Raman and infrared spectroscopic characterization of the arsenate-bearing mineral tangdanite– and in comparison with the discredited mineral clinotyrolite

The minerals clinotyrolite and fuxiaotuite are discredited in terms of the mineral tangdanite. The mixed anion mineral tangdanite Ca2Cu9(AsO4)4(SO4)0.5(OH)9 9H2O has been studied using a combination of Raman and infrared spectroscopy. Characteristic bands associated with arsenate, sulphate and hydroxyl units are identified. Broad bands in the OH stretching region are observed and are resolved into component bands. These bands are assigned to water and hydroxyl stretching vibrations. Two intense Raman bands at 837 and approximately 734 cm−1 are assigned to the ν1 (AsO4)3− symmetric stretching and ν3 (AsO4)3− antisymmetric stretching modes. Infrared bands at 1023 cm−1 are assigned to the (SO4)2− ν1 symmetric stretching mode, and infrared bands at 1052, 1110 and 1132 cm−1 assigned to (SO4)2− ν3 antisymmetric stretching modes, confirming the presence of the sulphate anion in the tangdanite structure. Raman bands at 593 and 628 cm−1 are attributed to the (SO4)2− ν4 bending modes. Low-intensity Raman bands found at 457 and 472 cm−1 are assigned to the (AsO4)3− ν2 bending modes. A comparison is made with the previously obtained spectral data on the discredited mineral clinotyrolite.

Infrared and Raman spectroscopic characterization of the carbonate bearing silicate mineral aerinite – Implications for the molecular structure

The mineral aerinite is an interesting mineral because it contains both silicate and carbonate units which is unusual. It is also a highly colored mineral being bright blue/purple. We have studied aerinite using a combination of techniques which included scanning electron microscopy, energy dispersive X-ray analysis, Raman and infrared spectroscopy. Raman bands at 1049 and 1072 cm−1 are assigned to the carbonate symmetric stretching mode. This observation supports the concept of the non-equivalence of the carbonate units in the structure of aerinite. Multiple infrared bands at 1354, 1390 and 1450 cm−1 supports this concept. Raman bands at 933 and 974 cm−1 are assigned to silicon–oxygen stretching vibrations. Multiple hydroxyl stretching and bending vibrations show that water is in different molecular environments in the aerinite structure.

A vibrational spectroscopic study of the phosphate mineral vantasselite Al4(PO4)3(OH)3·9H2O

We have studied the phosphate mineral vantasselite Al4(PO4)3(OH)3·9H2O using a combination of SEM with EDX and Raman and infrared spectroscopy. Qualitative chemical analysis shows Al, Fe and P. Raman bands at 1013 and 1027cm−1 are assigned to the PO43−ν1 symmetric stretching mode. The observation of two bands suggests the non-equivalence of the phosphate units in the vantasselite structure. Raman bands at 1051, 1076 and 1090cm−1 are attributed to the PO43−ν3 antisymmetric stretching vibration. A comparison is made with the spectroscopy of wardite. Strong infrared bands at 1044, 1078, 1092, 1112, 1133, 1180 and 1210cm−1 are attributed to the PO43−ν3 antisymmetric stretching mode. Some of these bands may be due to δAl2OH deformation modes. Vibrational spectroscopy offers a mechanism for the study of the molecular structure of vantasselite.

SEM, EDX and Raman and infrared spectroscopic study of brianyoungite Zn3(CO3,SO4)(OH)4 from Esperanza Mine, Laurion District, Greece

The mineral brianyoungite, a carbonate–sulphate of zinc, has been studied by scanning electron microscopy (SEM) with chemical analysis using energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Multiple carbonate stretching modes are observed and support the concept of non-equivalent carbonate units in the brianyoungite structure. Intense Raman band at 1056 cm−1 with shoulder band at 1038 cm−1 is assigned to the CO32− ν1 symmetric stretching mode. Two intense Raman bands at 973 and 984 cm−1 are assigned to the symmetric stretching modes of the SO42− anion. The observation of two bands supports the concept of the non-equivalence of sulphate units in the brianyoungite structure. Raman bands at 704 and 736 cm−1 are assigned to the CO32− ν4 bending modes and Raman bands at 507, 528, 609 and 638 cm−1 are assigned to the CO32− ν2 bending modes. Multiple Raman and infrared bands in the OH stretching region are observed, proving the existence of water and hydroxyl units in different molecular environments in the structure of brianyoungite. Vibrational spectroscopy enhances our knowledge of the molecular structure of brianyoungite.

A Raman and infrared spectroscopic study of the sulphate mineral aluminite Al2(SO4)(OH)4·7H2O

The mineral aluminite has been studied using a number of techniques, including scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a low intensity band at 1069 cm−1 which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3588 cm−1 is assigned to the OH unit stretching vibration and the broad feature at around 3439 cm−1 to water stretching bands. Water stretching vibrations are observed at 3157, 3294, 3378 and 3439 cm−1. Vibrational spectroscopy enables an assessment of the molecular structure of aluminite to be made.

Scanning electron microscopy with energy dispersive spectroscopy and Raman and infrared spectroscopic study of tilleyite Ca5Si2O7(CO3)2-Y

The mineral tilleyite-Y, a carbonate-silicate of calcium, has been studied by scanning electron microscopy with chemical analysis using energy dispersive spectroscopy (EDX) and Raman and infrared spectroscopy. Multiple carbonate stretching modes are observed and support the concept of non-equivalent carbonate units in the tilleyite structure. Multiple Raman and infrared bands in the OH stretching region are observed, proving the existence of water in different molecular environments in the structure of tilleyite. Vibrational spectroscopy offers new information on the mineral tilleyite.

A SEM, EDS and vibrational spectroscopic study of the tellurite mineral: Sonoraite Fe3+Te4+O3(OH)·H2O

We have undertaken a study of the tellurite mineral sonorite using electron microscopy with EDX combined with vibrational spectroscopy. Chemical analysis shows a homogeneous composition, with predominance of Te, Fe, Ce and In with minor amounts of S. Raman spectroscopy has been used to study the mineral sonoraite an examples of group A(XO3), with hydroxyl and water units in the mineral structure. The free tellurite ion has C3v symmetry and four modes, 2A1 and 2E. An intense Raman band at 734 cm−1 is assigned to the ν1 (TeO3)2− symmetric stretching mode. A band at 636 cm−1 is assigned to the ν3 (TeO3)2− antisymmetric stretching mode. Bands at 350 and 373 cm−1 and the two bands at 425 and 438 cm−1 are assigned to the (TeO3)2−ν2 (A1) bending mode and (TeO3)2−ν4 (E) bending modes. The sharp band at 3283 cm−1 assigned to the OH stretching vibration of the OH units is superimposed upon a broader spectral profile with Raman bands at 3215, 3302, 3349 and 3415 cm−1 are attributed to water stretching bands. The techniques of Raman and infrared spectroscopy are excellent for the study of tellurite minerals.

Raman and infrared spectroscopic study of turquoise minerals

Raman and infrared spectra of three well-defined turquoise samples, CuAl6(PO4)4(OH)8·4H2O, from Lavender Pit, Bisbee, Cochise county, Arizona; Kouroudaiko mine, Faleme river, Senegal and Lynch Station, Virginia were studied, interpreted and compared. Observed Raman and infrared bands were assigned to the stretching and bending vibrations of phosphate tetrahedra, water molecules and hydroxyl ions. Approximate O–H⋯O hydrogen bond lengths were inferred from the Raman and infrared spectra. No Raman and infrared bands attributable to the stretching and bending vibrations of (PO3OH)2− units were observed.

Raman and infrared spectroscopic characterization of the silicate mineral lamprophyllite

The mineral lamprophyllite is fundamentally a silicate based upon tetrahedral siloxane units with extensive substitution in the formula. Lamprophyllite is a complex group of sorosilicates with general chemical formula given as A2B4C2Si2O7(X)4, where the site A can be occupied by strontium, barium, sodium, and potassium; the B site is occupied by sodium, titanium, iron, manganese, magnesium, and calcium. The site C is mainly occupied by titanium or ferric iron and X includes the anions fluoride, hydroxyl, and oxide. Chemical composition shows a homogeneous phase, composed of Si, Na, Ti, and Fe. This complexity of formula is reflected in the complexity of both the Raman and infrared spectra. The Raman spectrum is characterized by intense bands at 918 and 940 cm−1. Other intense Raman bands are found at 576, 671, and 707 cm−1. These bands are assigned to the stretching and bending modes of the tetrahedral siloxane units.

Raman and infrared spectroscopic study of the borate mineral kaliborite

We have studied the mineral kaliborite. The sample originated from the Inder B deposit, Atyrau Province, Kazakhstan, and is part of the collection of the Geology Department of the Federal University of Ouro Preto, Minas Gerais, Brazil. The mineral is characterized by a single intense Raman band at 756 cm−1 assigned to the symmetric stretching modes of trigonal boron. Raman bands at 1229 and 1309 cm−1 are assigned to hydroxyl in-plane bending modes of boron hydroxyl units. Raman bands are resolved at 2929, 3041, 3133, 3172, 3202, 3245, 3336, 3398, and 3517 cm−1. These Raman bands are assigned to water stretching vibrations. A very intense sharp Raman band at 3597 cm−1 with a shoulder band at 3590 cm−1 is assigned to the stretching vibration of the hydroxyl units. The Raman data are complimented with infrared data and compared with the spectrum of kaliborite downloaded from the Arizona State University database. Differences are noted between the spectrum obtained in this work and that from the Arizona State University database. This research shows that minerals stored in a museum mineral collection age with time. Vibrational spectroscopy enhances our knowledge of the molecular structure of kaliborite.

The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China

Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1 km×1 km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.