pinecone/core-2020-05-10-deduplication huggingface dataset:
Comparison of seven portable Raman spectrometers : beryl as a case study

In this paper, a series of beryl varieties with the accent on emeralds was investigated using seven portable Raman spectrometers equipped mainly with 785- and 532-nm excitation lasers. Additionally, one dual system and a new portable sequentially shifted excitation Raman spectrometer were applied. The advantage of using handheld instrumentation for investigations to be carried out outside the laboratory is well documented. For major part of beryls (emeralds and aquamarines), the most intense Raman bands are found at correct positions +/-2 to 4cm(-1) using all the instruments (with the exception of one). Unambiguous identification of beryls is ensured by obtaining the strong characteristic of Raman features (1070 and 686 cm(-1)) of the whole spectrum. Spectroscopic performance and differences existing between the instruments not only from the construction and ergonomic point of view are discussed. All the instruments tested EzRaman-I Dual (Enwave Optronics), RaPort (EnSpectr), FirstGuard (Rigaku), FirstDefender XL and FirstDefender RM (Thermo Scientific), Inspector Raman (Delta Nu) and Bravo (Bruker) can be used for common gemmological and mineralogical work in situ. Two instruments (the RaPort and the sequentially shifted excitation Raman spectrometer Bravo) allow recording excellent quality Raman spectra comparable with laboratory dispersive Raman microspectrometers
Rigid-layer Raman-active modes in $N$-layer Transition Metal
  Dichalcogenides: interlayer force constants and hyperspectral Raman imaging

We report a comparative study of rigid layer Raman-active modes in $N$-layer
transition metal dichalcogenides. Trigonal prismatic (2Hc, such as MoSe$_2$,
MoTe$_2$, WS$_2$, WSe$_2$) and distorted octahedral (1T', such as ReS$_2$ and
ReSe$_2$) phases are considered. The Raman-active in-plane interlayer shear
modes and out-of-plane interlayer breathing modes appear as well-defined
features with wavenumbers in the range 0-40~cm$^{-1}$. These rigid layer modes
are well-described by an elementary linear chain model from which the
interlayer force constants are readily extracted. Remarkably, these force
constants are all found to be of the same order of magnitude. Finally, we show
that the prominent interlayer shear and breathing mode features allow
high-precision hyperspectral Raman imaging of $N-$layer domains within a given
transition metal dichalcogenide flake
Comparison of the Raman spectra of Bayerite, Boehmite, Diaspore and Gibbsite

Gibbsite and bayerite are alumina trihydrate (Al(OH) 3).  Gibbsite occurs abundantly in nature, usually as a major mineral component in bauxite whereas bayerite is rarely found in nature.  Boehmite and diaspore are alumina oxohydroxide (AlOOH) and are two other important minerals in bauxite.  The Raman spectra of these four minerals were obtained using a Fourier transform Raman spectrometer operating at 1064 nm. Bayerite spectrum shows five absorption bands, 3652, 3542, 3449, 3438, and 3421 cm-1 and the gibbsite spectrum shows four strong and sharp absorption bands, 3619, 3523, 3433 and 3363 cm-1 in the hydroxyl stretching region. Four broad bands, 3426, 3365, 3229 and 2935 cm-1 and three weak bands, 3420, 3216 and 3090 cm-1 are present in this region for diaspore and boehmite, respectively.  The Raman bands correspond well with the infrared absorption bands at 3620, 3525 cm-1 for gibbsite, 3365 cm-1 for diaspore and 3423, 3096 cm-1 for boehmite and these bands are assigned to be Raman and infrared active.  The spectra of bayerite, gibbsite and diaspore are complex while the spectrum of boehmite only illustrates four absorption bands in the low frequency region.  Common bands of RT-Raman spectra at 1019, 892, 816, 710, 568, 539, 506, 429, 395, 379, 321, 306, 255 and 242 cm-1 were observed for gibbsite, 1079, 1068, 898, 866, 545, 434, 388, 322, 292, 250 and 239 cm-1 for bayerite, 705, 608, 446, 260 and 216 cm-1 for diaspore, and 674, 495 and 360 cm-1 for boehmite.  The differences in the vibrational spectra of bayerite, gibbsite, diaspore and boehmite are interpreted as being due to the differences in the molecular structure of these minerals
Raman spectroscopic study of azurite and malachite at 298 and 77 K

Azurite {Cu2+3(CO3)2(OH)2} and malachite {Cu2+2(CO3)(OH)2}  are both monoclinic hydroxy carbonates of copper.  The Raman spectra of these two minerals have been collected at both 298 and 77 K together with the single crystal Raman spectra of azurite at 298 K.  The spectra of both azurite and malachite contain modes of three separate vibrational groups: OH, CO3 and Cu-O. Accordingly, for azurite the bands at 3453 and 3427 cm-1 have been assigned as the O-H stretching mode with the O-H bending modes found at 1035 and 952 cm-1. Malachite displays two hydroxyl stretching bands at 3474 and 3404 cm-1 at 298 K which shift to 3470 and 3400 cm-1 at 77 K while O-H out-of-plane bending modes are found at 1045 and 875 cm-1. For the carbonate group, bands are observed at 1090 cm-1 (ν1), 837 and 817 cm-1 (ν2), 1490 and 1415 cm-1 (ν 3), and 769 and 747 cm-1 (ν 4). The effect of collecting the spectra at 77 K results in considerable band narrowing.  The Raman spectra of the single crystals of azurite show the orientation dependence of the vibrational modes.  A mechanism for ν2 splitting is proposed whereby vertical carbonate ions couple to form an in-phase and out of phase bending modes. Combination of these vibrational modes such as ν 1 + ν 3, ν 1 + ν3, ν1 + ν4 and 2ν2 are found at 2530, 2414, 1860, and 1670 cm-1, respectively. IR bands for the Cu-O stretching modes are observed at 495 and 400 cm-1, while Cu-O bending modes occur at 455 and 345 cm-1. Bands at 305 and 240 cm-1 are assigned to the O-Cu-OH bending modes. The Raman out-of-plane bending modes are found at 194 and 170 cm-1. For the carbonate group, infrared bands are observed at 1095 cm-1 (ν1), 834 and 816 cm-1(ν2), 1430 and 1419 cm-1 (ν3) and  764 and 739 cm-1 (ν 4). Combination of the CO3 vibrational modes ν1 + ν4 is observed at 1860 cm-1. IR bands for Cu-O stretching modes are observed at 580, 570 and 505 cm-1
Raman spectroscopy of the phase-related basic copper arsenate minerals olivenite, cornwallite, cornubite and clinoclase

The Raman spectra of olivenite, cornwallite and its diamorph cornubite and clinoclase have been obtained at 298 and 77K using a combination of a thermal stage and Raman microscopy.  The vibrational spectra of minerals are different, in line with differences in crystal structure and composition. Some similarity in the Raman spectra of the hydroxyl-stretching region exists, particularly at 298 K. Two hydroxyl-stretching frequencies are observed for each mineral with the bands for clinoclase being well separated.  Characteristic differences in the OH deformation regions are observed.  Differences are also observed in the arsenate stretching and deformation regions.  The OAsO bending modes are identified.\ud
The application of Raman microscopy to the study of closely related mineral phases has enabled their molecular characterisation using their Raman spectrum, thus enabling the rapid identification of phases in complex mixtures of secondary copper arsenates from the oxidized zones of base metal ore bodies
Raman spectroscopy of the polyanionic copper(II) minerals buttgenbachite and connellite : implications for studies of ancient copper objects and bronzes

The minerals connellite and buttgenbachite, complex hydroxy sulfate-nitrates of Cu(II), are rare products formed during the corrosion of bronze and brass objects. Infrared and Raman spectra of buttgenbachite and connellite have been obtained at 298 and 77 K using a Raman microprobe in combination with a thermal stage. Raman spectra show the presence of nitrate, sulfate and chloride in the mineral. Spectra of the hydroxyl-stretching region are complex with multiple bands being observed. These observations are in agreement with the structure of the minerals in that the nitrate ion occupies two different sites and that six hydroxyl groups are crystallographically independent. Various OH stretching bands are attributed to independent hydroxyl units in the crystal structure and zeolitic water OH stretching modes. Raman spectroscopy is an excellent technique for the identification of these complex minerals and for the determination of the distribution of anions in their structure
Raman spectroscopy of the basic copper chloride minerals atacamite and paratacamite - implications for the study of copper, brass and bronze objects of archeological significance

Raman spectra of the basic copper chloride minerals atacamite and paratacamite have been obtained at 298 and 77K using a Raman microprobe in combination with a thermal stage. Four distinct regions involved with hydroxyl stretching, hydroxyl deformation, CuO stretching and CuCl stretching and bending have been identified. The implication from the study is that Raman spectroscopy can be a useful tool for identifying corrosion products of copper, brass and bronze objects of archaeological or antiquarian significance. In addition, the technique may be a useful aid in the restoration degraded pigment products from old paintings
Raman spectroscopy of synthetic erythrite, partially dehydrated erythrite and hydrothermally synthesized dehydrated erythrite

The Raman spectra of the mono, di and octa (commonly known as the mineral erythrite) hydrates of cobalt(II) arsenate synthesized using hydrothermal techniques were obtained. The hydrates can be distinguished by their water hydroxyl stretching bands. Splitting of the AsO stretching vibrations is observed in the 77 K spectrum. The band at 852 cm−1 is assigned to the ν1 symmetric stretching vibration and the band at 790 cm−1 to the ν3 antisymmetric stretching vibration. The low-wavenumber region was used to identify bands attributable to the ν4 and ν2 modes
Molecular structure of the adelite group of minerals - a Raman spectroscopic study

The application of Raman microscopy to the study of closely related mineral phases of the adelite group has enabled their molecular characterisation.  The adelite group of minerals are orthorhombic arsenates and vanadates of general formula AB2+(XO4)(OH) where X may be As5+ or V5+ and cation A may be Ca or Pb; cation B may be Co or Cu and others.  Raman spectroscopy has proven most powerful for the identification of these minerals.  In particular the position of the hydroxyl stretching vibrations and most of the arsenate bands have been identified.  The two minerals tangeite and calciovolborthite have previously been identified as the same mineral. Raman spectroscopy has proven that the minerals are not identical and have different structures.  The application of Raman spectroscopy to the study of these minerals shows that increased distortion of the arsenate anion occur as the cationic substitution from conichalcite to austinite to duftite occurs
Raman spectroscopic study of the basic copper sulphates-implications for copper corrosion and 'bronze disease'

The basic copper sulphates are of interest because of their appearance in many environmental situations such as copper pipe corrosion, restoration of brass and bronze objects, leaching from waste mineral dumps and the restoration of frescoes. The Raman spectra of the basic copper sulphate minerals antlerite, brochantite, posnjakite and langite are reported using a Nd-Yag laser operating at an excitation wavelength of 780 nm.  In line with their crystal structures, each basic copper sulphate mineral has its own characteristic Raman spectrum, which enables their identification.  Except for brochantite multiple bands are observed for the SO stretching vibration.  Similarly multiple bands are observed for the antisymmetric SO and OSO bending regions.  Hydroxyl deformation modes in the 730 to 790 cm-1 region are observed. The use of the HeNe laser operating at an excitation wavelength of 633 nm enabled the hydroxyl stretching bands of the minerals to be obtained.  Antlerite and brochantite are characterised by hydroxyl stretching bands at 3580 and 3488 cm-1.  The minerals posnjakite and langite display Raman hydroxyl-stretching vibrations at 3588 and 3564 cm-1.  The Raman spectra of these two minerals show water OH-stretching bands at 3405, 3372 and 3260 cm-1.  Raman spectroscopy allows the ready identification of these minerals
Isomorphic substitution in vanadinite [Pb5(VO4)3Cl]-a Raman spectroscopic study

The Raman and infrared spectroscopy of three vanadinite [Pb5(VO4)Cl] specimens from three localities has been studied. Single crystal Raman spectra were obtained and the spectra were found to be both orientation and temperature dependent. Measurement of the Raman spectra at liquid nitrogen temperature enabled better band separation and increased intensities of weak bands through band narrowing enabling, the assignment of the bands in vanadinites to be made.  Two types of isomorphous substitution are identified (a) substitution in the bulk of the crystal where electron beam microanalysis identifies the presence of calcium and copper. (b) surface substitution where infrared spectroscopy shows the isomorphous substitution of vanadate by phosphate and of chloride by hydroxyl groups
Broadening public participation in systematic reviews : a case example involving young people in two configurative reviews

Background: Arguments supporting the involvement of users in research have even more weight when involving the public in systematic reviews of research. We aimed to explore the potential for public involvement in systematic reviews of observational and qualitative studies.\ud
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Methods: Two consultative workshops were carried out with a group of young people (YP) aged 12–17 years to examine two ongoing reviews about obesity: one about children's views and one on the link between obesity and educational attainment. YP were invited to comment on the credibility of themes, to propose elements of interventions, to suggest links between educational attainment and obesity and to comment on their plausibility.\ud
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Results: Researchers had more confidence in review findings, after checking that themes identified as important by YP were emphasised appropriately. Researchers were able to use factors linking obesity and attainment identified as important by YP to identify limitations in the scope of extant research.\ud
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Conclusion: Consultative workshops helped researchers draw on the perspectives of YP when interpreting and reflecting upon two systematic reviews. Involving users in judging synthesis credibility and identifying concepts was easier than involving them in interpreting findings. Involvement activities for reviews should be designed with review stage, purpose and group in mind
Get real in individual participant data (IPD) meta-analysis: a review of the methodology.

Individual participant data (IPD) meta-analysis is an increasingly used approach for synthesizing and investigating treatment effect estimates. Over the past few years, numerous methods for conducting an IPD meta-analysis (IPD-MA) have been proposed, often making different assumptions and modeling choices while addressing a similar research question. We conducted a literature review to provide an overview of methods for performing an IPD-MA using evidence from clinical trials or non-randomized studies when investigating treatment efficacy. With this review, we aim to assist researchers in choosing the appropriate methods and provide recommendations on their implementation when planning and conducting an IPD-MA. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd
Sequential biases in accumulating evidence

Whilst it is common in clinical trials to use the results of tests at one phase to decide whether to continue to the next phase and to subsequently design the next phase, we show that this can lead to biased results in evidence synthesis. Two new kinds of bias associated with accumulating evidence, termed "sequential decision bias" and "sequential design bias" are identified. Both kinds of bias are the result of making decisions on the usefulness of a new study, or its design, based on the previous studies. Sequential decision bias is determined by the correlation between the value of the current estimated effect and the probability of conducting an additional study. Sequential design bias arises from using the estimated value instead of the clinically relevant value of an effect in sample size calculations. We considered both the fixed effect and the random effects models of meta-analysis, and demonstrated analytically and by simulations that in both settings the problems due to sequential biases are apparent. According to our simulations, the sequential biases increase with increased heterogeneity. Minimisation of sequential biases arises as a new and important research area necessary for successful evidence-based approaches to the development of science
Detecting outlying studies in meta-regression models using a forward search algorithm

When considering data from many trials, it is likely that some of them present a markedly different intervention effect or exert an undue influence on the summary results. We develop a forward search algorithm for identifying outlying and influential studies in meta-analysis models. The forward search algorithm starts by fitting the hypothesized model to a small subset of likely outlier-free studies and proceeds by adding studies into the set one-by-one that are determined to be closest to the fitted model of the existing set. As each study is added to the set, plots of estimated parameters and measures of fit are monitored to identify outliers by sharp changes in the forward plots. We apply the proposed outlier detection method to two real data sets; a metaanalysis of 26 studies that examines the effect of writing-to-learn interventions on academic achievement adjusting for three possible effect modifiers, and a meta-analysis of 70 studies that compares a fluoride toothpaste treatment to placebo for preventing dental caries in children. A simple simulated example is used to illustrate the steps of the proposed methodology and a small scale simulation study is conducted to evaluate the performance of the proposed method
GetReal in mathematical modelling: a review of studies predicting drug effectiveness in the real world.

The performance of a drug in a clinical trial setting often does not reflect its effect in daily clinical practice. In this third of three reviews, we examine the applications that have been used in the literature to predict real-world effectiveness from randomized controlled trial efficacy data. We searched MEDLINE, EMBASE from inception to March 2014, the Cochrane Methodology Register, and websites of key journals and organisations and reference lists. We extracted data on the type of model and predictions, data sources, validation and sensitivity analyses, disease area and software. We identified 12 articles in which four approaches were used: multi-state models, discrete event simulation models, physiology-based models and survival and generalized linear models. Studies predicted outcomes over longer time periods in different patient populations, including patients with lower levels of adherence or persistence to treatment or examined doses not tested in trials. Eight studies included individual patient data. Seven examined cardiovascular and metabolic diseases and three neurological conditions. Most studies included sensitivity analyses, but external validation was performed in only three studies. We conclude that mathematical modelling to predict real-world effectiveness of drug interventions is not widely used at present and not well validated. © 2016 The Authors Research Synthesis Methods Published by John Wiley & Sons Ltd
Accounting for heterogeneity in meta-analysis using a multiplicative model-an empirical study

Following the embargo period the above license applies.In meta-analysis, the random-effects model is often used to account for heterogeneity. The model assumes that heterogeneity has an additive effect on the variance of effect sizes. An alternative model, which assumes multiplicative heterogeneity, has been little used in the medical statistics community, but is widely used by particle physicists. In this paper, we compare the two models using a random sample of 448 meta-analyses drawn from the Cochrane Database of Systematic Reviews. In general, differences in goodness of fit are modest. The multiplicative model tends to give results that are closer to the null, with a narrower confidence interval. Both approaches make different assumptions about the outcome of the meta-analysis. In our opinion, the selection of the more appropriate model will often be guided by whether the multiplicative model's assumption of a single effect size is plausible. Copyright © 2016 John Wiley & Sons, Ltd.Peer-reviewedPost-prin
Meta-analysis of few small studies in orphan diseases

Meta-analyses in orphan diseases and small populations generally face
particular problems including small numbers of studies, small study sizes, and
heterogeneity of results. However, the heterogeneity is difficult to estimate
if only very few studies are included. Motivated by a systematic review in
immunosuppression following liver transplantation in children we investigate
the properties of a range of commonly used frequentist and Bayesian procedures
in extensive simulation studies. Furthermore, the consequences for interval
estimation of the common treatment effect in random effects meta-analysis are
assessed. The Bayesian credibility intervals using weakly informative priors
for the between-trial heterogeneity exhibited coverage probabilities in excess
of the nominal level for a range of scenarios considered. However, they tended
to be shorter than those obtained by the Knapp-Hartung method, which were also
conservative. In contrast, methods based on normal quantiles exhibited
coverages well below the nominal levels in many scenarios. With very few
studies, the performance of the Bayesian credibility intervals is of course
sensitive to the specification of the prior for the between trial
heterogeneity. In conclusion, the use of weakly informative priors as
exemplified by half-normal priors (with scale 0.5 or 1.0) for log odds ratios
is recommended for applications in rare diseases.Comment: 23 pages, 6 figures, 3 table
Sequential change detection and monitoring of temporal trends in random-effects meta-analysis

Temporal changes in magnitude of effect sizes reported in many areas of research are a threat to the credibility of the results and conclusions of meta-analysis. Numerous sequential methods for meta-analysis have been proposed to detect changes and monitor trends in effect sizes so that meta-analysis can be updated when necessary and interpreted based on the time it was conducted. The difficulties of sequential meta-analysis under the random-effects model are caused by dependencies in increments introduced by the estimation of the heterogeneity parameter τ2. In this paper we propose the use of a retrospective CUSUM-type test with bootstrap critical values. This method allows retrospective analysis of the past trajectory of cumulative effects in random-effects meta-analysis, and its visualisation on a chart similar to CUSUM chart. Simulation results show that the new method demonstrates good control of Type I error regardless of the number or size of the studies and the amount of heterogeneity. Application of the new method is illustrated on two examples of medical meta-analyses