bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal structure and topological affinities of magbasite, KBaFe3+Mg7Si8O22(OH)2F6: a trellis structure related to amphibole and carpholite
Authors: Welch M. D. , Mitchell R. H. , Kampf A. R. , Chakhmouradian A. R. , Smith D. , Carter M. 
Published: March 2014

AbstractThe crystal structure of magbasite from the Eldor carbonatite complex, Quebec, Canada, has been determined and indicates that the currently accepted formula should be revised to KBaFe3+Mg7Si8O22(OH)2F6. Magbasite is orthorhombic, space group Cmme (Cmma), with unit-cell parameters a 18.9506(3) Å, b 22.5045(3) Å, c 5.2780(1) Å, V 2250.93(6) Å3 (Z = 4). The structure has been solved and refined to final agreement indices R1 = 0.026, wR2 = 0.052, GooF = 1.116 for a total of 2379 unique reflections, and is a new kind of trellis motif related to amphibole and carpholite topologies. An amphibole-like I-beam ‖(100) of edge-sharing octahedrally-coordinated M(1,2,3) sites, which are filled by Mg, is sandwiched between double-chains of SiO4 tetrahedra ‖c. This I-beam is connected to side-ribbons ‖(010) of edge-sharing (Mg,Fe2+)O4(OH,F)2 and Fe3+O4(OH)2 octahedra to form a tunnelled box or trellis structure very like that of carpholite, for which the I-beams are pyroxene-like. K occupies a tunnel site analogous to the A site of amphibole. Ba occupies a cavity site at the corners where the I-beam and side-ribbon meet, and corresponds to the A site of carpholite. The structural relations between magbasite and carpholite are discussed.
Mercury-arsenic sulfosalts from the Apuan Alps (Tuscany, Italy). II. Arsiccioite, AgHg2TlAs2S6, a new mineral from the Monte Arsiccio mine: occurrence, crystal structure and crystal chemistry of the routhierite isotypic series
Authors: Biagioni C. , Bonaccorsi E. , Moëlo Y. , Orlandi P. , Bindi L. , D’Orazio M. , Vezzoni S. 
Published: March 2014

AbstractThe new mineral species arsiccioite, AgHg2TlAs2S6, was discovered in the baryte-pyrite-iron oxide ore deposit exploited at the Monte Arsiccio mine, near Sant’Anna di Stazzema (Apuan Alps, Tuscany, Italy). It occurs as anhedral grains scattered in microcrystalline baryte, associated with cinnabar, laffittite, protochabournéite, pyrite, realgar, Hg-bearing sphalerite and stibnite. Arsiccioite is red, with a metallic to sub-metallic lustre. Minimum and maximum reflectance data for COM wavelengths in air are [λ (nm):R(%)]: 471.1: 29.0/29.4; 548.3: 27.6/28.3; 586.6: 26.1/26.5; 652.3: 24.2/24.6. Electron microprobe analyses give (wt.%): Cu 0.78(6), Ag 8.68(21), Zn 0.47(27), Fe 0.04(1), Hg 35.36(87), Cd 0.20(5), Tl 18.79(33), As 10.77(19), Sb 4.75(10), S 18.08(21), Se 0.07(5), total 97.99(44). On the basis of ΣMe= 6 a.p.f.u., the chemical formula is Ag0.87(2)Cu0.13(1)Zn0.08(4)Fe0.01(1)Hg1.91(5)Cd0.02(1)Tl1.00(2)(As1.56(2)Sb0.42(1))S1.98S6.12(6)Se0.01(1). Arsiccioite is tetragonal,I2m, witha10.1386(6),c11.3441(5) Å,V1166.1(2) Å3,Z= 4. The main diffraction lines of the powder diagram are [d(in Å), visually estimated intensity,hkl]: 4.195, m, 211; 3.542, m, 103; 3.025, vs, 222; 2.636, m, 114; 2.518, s, 400 and 303. The crystal structure of arsiccioite has been refined by single-crystal X-ray data to a finalR1= 0.030, on the basis of 893 observed reflections. It shows a three dimensional framework of (Hg,Ag)- centred tetrahedra (1M1 + 2M2), with channels parallel to [001] hosting TlS6and (As,Sb)S3 disymmetric polyhedra. Arsiccioite is derived from its isotype routhieriteM1CuM2Hg2TlAs2S6through the double heterovalent substitutionM1Cu++M2Hg2+→M1Hg2++M2Ag+. This substitution obeys a steric constraint, with Ag+, the largest cation relative to Hg2+and Cu+, entering the largestM2 site. The ideal crystal chemical formula of arsiccioite isM1HgM2(Hg0.5Ag0.5)2TlAs2S6. The crystal chemistry of the routhierite isotypic series is discussed. Finally, the distribution of Hg ore minerals in the Apuan Alps is reviewed.
Klajite, MnCu4(AsO4)2(AsO3OH)2(H2O)10, from Jáchymov (Czech Republic): the second world occurrence
Authors: Plášil J. , Kasatkin A. V. , Škoda R. , Škácha P. 
Published: March 2014

AbstractKlajite, MnCu4(AsO4)2(AsO3OH)2(H2O)10, the Mn-Cu-bearing member of the lindackerite group, was found in Jáchymov, Czech Republic, as the second world occurrence. It is associated with ondrušite and other arsenate minerals growing on the quartz gangue with disseminated primary sulfides, namely tennantite and chalcopyrite. Electron-microprobe data showed klajite aggregates to be chemically inhomogeneous at larger scales, varying from Mn-Ca-rich to Cu-rich domains. The chemical composition of the the Mn-rich parts of aggregates can be expressed by the empirical formula (Mn0.46Ca0.22Cu0.07Mg0.02)∑0.77(Cu3.82Mg0.14Ca0.03Zn0.01)∑4.00(As1.94Si0.06)∑2.00O8[AsO2.73(OH)1.27]2(H2O)10 (mean of seven representative spots; calculated on the basis of As + Si + P = 4 a.p.f.u. (atoms per formula unit) and 10 H2O from ideal stoichiometry), showing a slight cationic deficiency at the key Me-site. According to single-crystal X-ray diffraction, klajite from Jáchymov is triclinic, P , with a = 6.4298(8), b = 7.9716(8), c = 10.707(2) Å, α = 85.737(12)°, β = 80.994(13)°, γ = 84.982(10)°, and V = 538.85(14) Å3, Z = 1. The crystal structure was refined to R1 = 0.0628 for 1034 unique observed reflections (with Iobs > 3σ(I)), confirming that klajite (Mn-Cu member) and ondrušite (Ca-Cu member) are isostructural. The current data-set allowed determination of the positions of several hydrogen atoms. Discussion on hydrogen bonding networks in the structure of klajite as well as detailed bond-valence analysis are provided.
Therasiaite, (NH4)3KNa2Fe2+Fe3+(SO4)3Cl5, a new sulfate chloride from La Fossa Crater, Vulcano, Aeolian islands, Italy
Authors: Demartin F. , Castellano C. , Campostrini I. 
Published: March 2014

AbstractThe new mineral therasiaite, ideally (NH4)3KNa2Fe2+Fe3+(SO4)3Cl5, was found in a mediumtemperature (∼250°C) intracrater active fumarole at La Fossa crater, Vulcano, Aeolian Islands, Sicily, Italy. It occurs on a pyroclastic breccia as brown to dark brown equant to short prismatic crystals up to 0.1 mm in length, in association with salammoniac, kremersite and adranosite. The mineral is monoclinic, space group: Cc (no. 9) with a = 18.284(4), b = 12.073(2), c = 9.535(2) Å, β = 108.10(3)°, V = 2000.6(7) Å3 and Z = 4. The six strongest reflections in the X-ray powder diffraction pattern are: [dobs in Å(I)(hkl)] 2.812(100)(23), 2.664(77)(13), 3.297(28)(33), 3.208(14)(2), 3.008(12)(040), 2.942(11)(331). The empirical formula (based on 17 anions per formula unit (p.f.u.)) is (NH4)2.68K1.32Na2.04Fe1.76Al0.12Mn0.12S2.98O11.95Cl5.05. The measured density is 2.41(1) g cm−3, dcalc = 2.395 g cm−3. The mineral is biaxial (−) with α= 1.585(3) β = 1.615(3) and γ = 1.630(3) (white light). Using single-crystal diffraction data, the structure was refined to a final R(F) = 0.0240 for 5574 independent observed reflections [I > 2σ(I)]. The structure of therasiaite displays a novel topology and contains two independent, distorted octahedral Fe sites, with the Fe atoms in oxidation state 3+ and 2+, respectively, each surrounded by three Cl atoms and three oxygens of the sulfate ions. The Fe octahedra and the three independent sulfate anions are connected to form chains running along [001]. Voids between the chains are occupied by three independent ammonium ions (partially replaced by K+), one K+ and two Na+ ions. The formula resulting from the structure refinement is [(NH4)2.25K0.75]KNa2Fe2(SO4)3Cl5.
A novel early precursor cell population from rat bone marrow promotes angiogenesis in vitro
Authors: Brandl Andreas , Yuan Quan , Boos Anja M , Beier Justus P , Arkudas Andreas , Kneser Ulrich , Horch Raymund E , Bleiziffer Oliver 
Published: March 2014

Abstract

Background
Some studies demonstrated therapeutic angiogenesis attributable to the effects of endothelial progenitor cells (EPC), others have reported disappointing results. This may be due to the fact that EPC populations used in these contradictory studies were selected and defined by highly variable and differing experimental protocols. Indeed, the isolation and reliable characterization of ex vivo differentiated EPC raises considerable problems due to the fact there is no biomarker currently available to specifically identify EPC exclusively. On the other hand traditional differentiation of primary immature bone marrow cells towards the endothelial lineage is a time-consuming process of up to 5 weeks. To circumvent these shortcomings, we herein describe a facile method to isolate and enrich a primary cell population from rat bone marrow, combining differential attachment methodology with cell sorting technology.

Results
The combination of these techniques enabled us to obtain a pure population of early endothelial precursor cells that show homogenous upregulation of CD31 and VEGF-R2 and that are positive for CD146. These cells exhibited typical sprouting on Matrigel™. Additionally, this population displayed endothelial tube formation when resuspended in Matrigel™ as well as in fibrin glue, demonstrating its functional angiogenic capacity. Moreover, these cells stained positive for DiI-ac-LDL and FITC-UEA, two markers that are commonly considered to stain differentiating EPCs. Based upon these observations in this study we describe a novel and time-saving method for obtaining a pure endothelial precursor cell population as early as 2–3 weeks post isolation that exhibits endothelial abilities in vitro and which still might have retained its early endothelial lineage properties.

Conclusion
The rapid isolation and the high angiogenic potential of these syngeneic cells might facilitate and accelerate the pre-vascularization of transplanted tissues and organs also in a human setting in the future.
Effects of cytosine methylation on transcription factor binding sites
Authors: Medvedeva Yulia A , Khamis Abdullah M , Kulakovskiy Ivan V , Ba-Alawi Wail , Bhuyan Md Shariful I , Kawaji Hideya , Lassmann Timo , Harbers Matthias , Forrest Alistair RR , Bajic Vladimir B ,   The FANTOM consortium
Published: March 2014

Abstract

Background
DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.

Results
We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines “traffic lights”. We observed a strong selection against CpG “traffic lights” within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.

Conclusions
Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription.
Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle
Authors: Killeen Aideen P , Morris Dermot G , Kenny David A , Mullen Michael P , Diskin Michael G , Waters Sinéad M 
Published: March 2014

Abstract

Background
In both beef and dairy cattle, the majority of early embryo loss occurs within the first 14 days following insemination. During this time-period, embryos are completely dependent on their maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to their survival. The objective of this study was to investigate whether differences in endometrial gene expression during the mid-luteal phase of the estrous cycle exist between crossbred beef heifers ranked as either high (HF) or low fertility (LF) (following four rounds of artificial insemination (AI)) using the Affymetrix® 23 K Bovine Gene Chip.

Results
Conception rates for each of the four rounds of AI were within a normal range: 70–73.3%. Microarray analysis of endometrial tissue collected on day 7 of the estrous cycle detected 419 differentially expressed genes (DEG) between HF (n = 6) and LF (n = 6) animals. The main gene pathways affected were, cellular growth and proliferation, angiogenesis, lipid metabolism, cellular and tissue morphology and development, inflammation and metabolic exchange. DEG included, FST, SLC45A2, MMP19, FADS1 and GALNT6.

Conclusions
This study highlights, some of the molecular mechanisms potentially controlling uterine endometrial function during the mid-luteal phase of the estrous cycle, which may contribute to uterine endometrial mediated impaired fertility in cattle. Differentially expressed genes are potential candidate genes for the identification of genetic variation influencing cow fertility, which may be incorporated into future breeding programmes.
Immature articular cartilage and subchondral bone covered by menisci are potentially susceptive to mechanical load
Authors: Iijima Hirotaka , Aoyama Tomoki , Ito Akira , Tajino Junichi , Nagai Momoko , Zhang Xiangkai , Yamaguchi Shoki , Akiyama Haruhiko , Kuroki Hiroshi 
Published: March 2014

Abstract

Background
The differences of mechanical and histological properties between cartilage covered by menisci and uncovered by menisci may contribute to the osteoarthritis after meniscectomy and these differences are not fully understood. The purpose of this study is to investigate potential differences in the mechanical and histological properties, and in particular the collagen architecture, of the superficial cartilage layer and subchondral bone between regions covered and uncovered by menisci using immature knee.

Methods
Osteochondral plugs were obtained from porcine tibial cartilage that was either covered or uncovered by menisci. Investigation of the thickness, mechanical properties, histology, and water content of the cartilage as well as micro-computed tomography analysis of the subchondral bone was performed to compare these regions. Collagen architecture was also assessed by using scanning electron microscopy.

Results
Compared to the cartilage uncovered by menisci, that covered by menisci was thinner and showed a higher deformity to compression loading and higher water content. In the superficial layer of cartilage in the uncovered regions, collagen fibers showed high density, whereas they showed low density in covered regions. Furthermore, subchondral bone architecture varied between the 2 regions, and showed low bone density in covered regions.

Conclusions
Cartilage covered by menisci differed from that uncovered in both its mechanical and histological properties, especially with regards to the density of the superficial collagen layer. These regional differences may be related to local mechanical environment in normal condition and indicate that cartilage covered by menisci is tightly guarded by menisci from extreme mechanical loading. Our results indicate that immature cartilage degeneration and subchondral microfracture may occur easily to extreme direct mechanical loading in covered region after meniscectomy.
A machine learning framework for TCP round-trip time estimation
Authors: Arouche Nunes Bruno Astuto , Veenstra Kerry , Ballenthin William , Lukin Stephanie , Obraczka Katia 
Published: March 2014

Abstract
In this paper, we explore a novel approach to end-to-end round-trip time (RTT) estimation using a machine-learning technique known as the experts framework. In our proposal, each of several ‘experts’ guesses a fixed value. The weighted average of these guesses estimates the RTT, with the weights updated after every RTT measurement based on the difference between the estimated and actual RTT.
Through extensive simulations, we show that the proposed machine-learning algorithm adapts very quickly to changes in the RTT. Our results show a considerable reduction in the number of retransmitted packets and an increase in goodput, especially in more heavily congested scenarios. We corroborate our results through ‘live’ experiments using an implementation of the proposed algorithm in the Linux kernel. These experiments confirm the higher RTT estimation accuracy of the machine learning approach which yields over 40% improvement when compared against both standard transmission control protocol (TCP) as well as the well known Eifel RTT estimator. To the best of our knowledge, our work is the first attempt to use on-line learning algorithms to predict network performance and, given the promising results reported here, creates the opportunity of applying on-line learning to estimate other important network variables.
Implementation of fast HEVC encoder based on SIMD and data-level parallelism
Authors: Ahn Yong-Jo , Hwang Tae-Jin , Sim Dong-Gyu , Han Woo-Jin 
Published: March 2014

Abstract
This paper presents several optimization algorithms for a High Efficiency Video Coding (HEVC) encoder based on single instruction multiple data (SIMD) operations and data-level parallelism. Based on the analysis of the computational complexity of HEVC encoder, we found that interpolation filter, cost function, and transform take around 68% of the total computation, on average. In this paper, several software optimization techniques, including frame-level interpolation filter and SIMD implementation for those computationally intensive parts, are presented for a fast HEVC encoder. In addition, we propose a slice-level parallelization and its load-balancing algorithm on multi-core platforms from the estimated computational load of each slice during the encoding process. The encoding speed of the proposed parallelized HEVC encoder is accelerated by approximately ten times compared to the HEVC reference model (HM) software, with minimal loss of coding efficiency.
Bioprospecting for acidophilic lipid-rich green microalgae isolated from abandoned mine site water bodies
Authors: Eibl Joseph K , Corcoran Jason D , Senhorinho Gerusa N A , Zhang Kejian , Hosseini Nekoo Seyed , Marsden James , Laamanen Corey A , Scott John A , Ross Gregory M 
Published: March 2014

Abstract
With fossil fuel sources in limited supply, microalgae show tremendous promise as a carbon neutral source of biofuel. Current microalgae biofuel strategies typically rely on growing high-lipid producing laboratory strains of microalgae in open raceways or closed system photobioreactors. Unfortunately, these microalgae species are found to be sensitive to environmental stresses or competition by regional strains. Contamination by invasive species can diminish productivity of commercial algal processes. A potential improvement to current strategies is to identify high-lipid producing microalgae, which thrive in selected culture conditions that reduce the risk of contamination, such as low pH. Here we report the identification of a novel high-lipid producing microalgae which can tolerate low pH growth conditions. Lig 290 is a Scenedesmus spp. isolated from a low pH waterbody (pH = 4.5) in proximity to an abandoned lignite mine in Northern Ontario, Canada. Compared to a laboratory strain of Scendesmus dimorphus, Lig 290 demonstrated robust growth rates, a strong growth profile, and high lipid production. As a consequence, Lig 290 may have potential application as a robust microalgal species for use in biofuel production.
Sex hormone associations with breast cancer risk and the mediation of randomized trial postmenopausal hormone therapy effects
Authors: Zhao Shanshan , Chlebowski Rowan T , Anderson Garnet L , Kuller Lewis H , Manson JoAnn E , Gass Margery , Patterson Ruth , Rohan Thomas E , Lane Dorothy S , Beresford Shirley AA , Lavasani Sayeh , Rossouw Jacques E , Prentice Ross L 
Published: March 2014

Abstract
Introduction
Paradoxically, a breast cancer risk reduction with conjugated equine estrogens (CEE) and a risk elevation with CEE plus medroxyprogesterone acetate (CEE + MPA) were observed in the Women’s Health Initiative (WHI) randomized controlled trials. The effects of hormone therapy on serum sex hormone levels, and on the association between baseline sex hormones and disease risk, may help explain these divergent breast cancer findings.

Methods
Serum sex hormone concentrations were measured for 348 breast cancer cases in the CEE + MPA trial and for 235 cases in the CEE trial along with corresponding pair-matched controls, nested within the WHI trials of healthy postmenopausal women. Association and mediation analyses, to examine the extent to which sex hormone levels and changes can explain the breast cancer findings, were conducted using logistic regression.

Results
Following CEE treatment, breast cancer risk was associated with higher concentrations of baseline serum estrogens, and with lower concentrations of sex hormone binding globulin. However, following CEE + MPA, there was no association of breast cancer risk with baseline sex hormone levels. The sex hormone changes from baseline to year 1 provided an explanation for much of the reduced breast cancer risk with CEE. Specifically, the treatment odds ratio (95% confidence interval) increased from 0.71 (0.43, 1.15) to 0.92 (0.41, 2.09) when the year 1 measures were included in the logistic regression analysis. In comparison, the CEE + MPA odds ratio was essentially unchanged when these year 1 measures were included.

Conclusions
Breast cancer risk remains low following CEE use among women having favorable baseline sex hormone profiles, but CEE + MPA evidently produces a breast cancer risk for all women similar to that for women having an unfavorable baseline sex hormone profile. These patterns could reflect breast ductal epithelial cell stimulation by CEE + MPA that is substantially avoided with CEE, in conjunction with relatively more favorable effects of either regimen following a sustained period of estrogen deprivation. These findings may have implications for other hormone therapy formulations and routes of delivery.

Trial registration
clinicaltrials.gov identifier: NCT00000611.