bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Amplified Fragment Length Polymorphism To Identify 42
Cladophialophora
Strains Related to Cerebral Phaeohyphomycosis with In Vitro Antifungal Susceptibility
Authors: Badali Hamid , de Hoog G. Sybren , Curfs-Breuker Ilse , Klaassen Corné H. W. , Meis Jacques F. 
Published: April 2010

ABSTRACT

The amplified fragment length polymorphism technique has been applied to identify neurotropic chaetothyrialean black yeasts and relatives from clinical sources.
Cladophialophora bantiana
,
C. emmonsii
,
C. arxii
,
C. devriesii
, and
C. modesta
, previously identified on the basis of sequencing and phenotypic and physiological criteria, were confirmed by cluster analysis, demonstrating the clear separation of
C. bantiana
as a rather homogeneous group from the other species.
C. bantiana
is a neurotropic fungus causing cerebral abscesses with a mortality of up to 70%. Successful therapy consists of neurosurgical intervention and optimal antifungal therapy. Since the latter is not clearly defined in a large series, we tested the
in vitro
activities of eight antifungal drugs against clinical isolates of
C. bantiana
(
n
= 37),
C. modesta
(
n
= 2),
C. arxii
(
n
= 1),
C. emmonsii
(
n
= 1), and
C. devriesii
(
n
= 1), all of which had caused invasive infections. The resulting MIC
90
s for all neurotropic
C. bantiana
strains were as follows, in increasing order: posaconazole, 0.125 μg/ml; itraconazole, 0.125 μg/ml; isavuconazole, 0.5 μg/ml; amphotericin B, 1 μg/ml; voriconazole, 2 μg/ml; anidulafungin, 2 μg/ml; caspofungin, 4 μg/ml; and fluconazole, 64 μg/ml. On the basis of these
in vitro
results and the findings of previous clinical and animal studies, posaconazole seems to be a good alternative to the standard treatment, amphotericin B, for
C. bantiana
cerebral infections. The new agent isavuconazole, which is also available as an intravenous preparation, has adequate activity against
C. bantiana
.
Breakthrough Invasive Candidiasis in Patients on Micafungin
Authors: Pfeiffer Christopher D. , Garcia-Effron Guillermo , Zaas Aimee K. , Perfect John R. , Perlin David S. , Alexander Barbara D. 
Published: April 2010

ABSTRACT

For
Candida
species, a bimodal wild-type MIC distribution for echinocandins exists, but resistance to echinocandins is rare. We characterized isolates from patients with invasive candidiasis (IC) breaking through ≥3 doses of micafungin therapy during the first 28 months of its use at our center: MICs were determined and hot-spot regions within
FKS
genes were sequenced. Eleven of 12 breakthrough IC cases identified were in transplant recipients. The median duration of micafungin exposure prior to breakthrough was 33 days (range, 5 to 165). Seventeen breakthrough isolates were recovered:
FKS
hot-spot mutations were found in 5
C. glabrata
and 2
C. tropicalis
isolates; of these, 5 (including all
C. glabrata
isolates) had micafungin MICs of >2 μg/ml, but all demonstrated caspofungin MICs of >2 μg/ml. Five
C. parapsilosis
isolates had wild-type
FKS
sequences and caspofungin MICs of 0.5 to 1 μg/ml, but 4/5 had micafungin MICs of >2 μg/ml. The remaining isolates retained echinocandin MICs of ≤2 μg/ml and wild-type
FKS
gene sequences. Breakthrough IC on micafungin treatment occurred predominantly in severely immunosuppressed patients with heavy prior micafungin exposure. The majority of cases were due to
C. glabrata
with an
FKS
mutation or wild-type
C. parapsilosis
with elevated micafungin MICs. MIC testing with caspofungin identified all mutant strains. Whether the naturally occurring polymorphism within the
C. parapsilosis FKS1
gene responsible for the bimodal wild-type MIC distribution is also responsible for micafungin MICs of >2 μg/ml and clinical breakthrough or an alternative mechanism contributes to the nonsusceptible echinocandin MICs in
C. parapsilosis
requires further study.
Characterization of Epidemiologically Unrelated
Acinetobacter baumannii
Isolates from Four Continents by Use of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Sequence-Based Typing of
bla
OXA-51-like
Genes
Authors: Hamouda Ahmed , Evans Benjamin A. , Towner Kevin J. , Amyes Sebastian G. B. 
Published: April 2010

ABSTRACT

This study used a diverse collection of epidemiologically unrelated
Acinetobacter baumannii
isolates to compare the robustness of a multilocus sequence typing (MLST) scheme, based on conserved regions of seven housekeeping genes,
gltA
,
gdhB
,
recA
,
cpn60
,
rpoD
, g
yrB
, and
gpi
, with that of sequence-based typing of
bla
OXA-51-like
genes (SBT-
bla
OXA-51-like
genes). The data obtained by analysis of MLST and SBT-
bla
OXA-51-like
genes were compared to the data generated by pulsed-field gel electrophoresis (PFGE). The topologies of the phylogenetic trees generated for the
gyrB
and
gpi
genes showed evidence of recombination and were inconsistent with those of the trees generated for the other five genes. MLST identified 24 sequence types (STs), of which 19 were novel, and 5 novel alleles. Clonality was demonstrated by eBURST analysis and standardized index of association values of >1 (
P
< 0.001). MLST data revealed that all isolates harboring the major
bla
OXA-51-like
alleles OXA-66, OXA-69, and OXA-71 fell within the three major European clonal lineages. However, the MLST data were not always in concordance with the PFGE data, and some isolates containing the same
bla
OXA-51-like
allele demonstrated <50% relatedness by PFGE. It was concluded that the g
yrB
and
gpi
genes are not good candidates for use in MLST analysis and that a SBT-
bla
OXA-51-like
gene scheme produced results comparable to those produced by MLST for the identification of the major epidemic lineages, with the advantage of having a significantly reduced sequencing cost and time. It is proposed that studies of
A. baumannii
epidemiology could involve initial screening of
bla
OXA-51-like
alleles to identify isolates belonging to major epidemic lineages, followed by MLST analysis to categorize isolates from common lineages, with PFGE being reserved for fine-scale typing.
NON-CIRCULAR CHAIN RING ALLOWS A REDUCTION OF JOINT LOADING IN CYCLING
Authors: BISI MARIA CRISTINA , STAGNI RITA , GNUDI GIANNI , CAPPELLO ANGELO 
Published: April 2010

Non-circular (NC) chain rings were primarily designed to improve the mechanical effectiveness of cycling. Their use can be investigated for application in rehabilitation: they could provide a solution to design an effective exercise reducing joint loading. The aim of this study was to analyze the differences in kinematics, energy consumption, and joint moments between circular and NC chain rings, then to identify a profile that can reduce joint loads, maintaining equal mechanical and metabolic works. Five young participants performed two tests on a cycloergometer; one with a circular chain ring and the other with an NC one. The test consisted in 15 min of cycling; during which they were asked to cycle at three different speeds and at two different powers. Stereophotogrammetric and metabolic data were acquired. Statistical analysis was applied on metabolic data. Joint angular velocities were obtained from kinematic data. A two-dimensional (2D) model of cycling was designed to estimate joint moments with both chain rings. A different ring profile was suggested to further reduce joint flexion peak moment. NC chain ring allows a reduction of flexion joint moments with respect to the circular one without significant difference in metabolic and kinematic data. The new profile proposed further decreases maximum knee flexion moment maintaining equal mechanical work.
HIGH-SPEED AND SECURE ENCRYPTION SCHEMES BASED ON CHINESE REMAINDER THEOREM FOR STORAGE AND TRANSMISSION OF MEDICAL INFORMATION
Authors: AITHAL GANESH , HARI BHAT K. N. , ACHARYA U. SRIPATI 
Published: April 2010

Medical records generated in hospitals often contain private and sensitive information. This privileged information must be prevented from falling into wrong hands. Thus, there is a strong need for developing a secure cryptographic scheme that can be adapted to use in conjunction with transmission and storage of medical information. Previous approaches have proposed the use of the advanced encryption standard (AES) algorithm for this purpose. In this article, we are proposing a new robust, high-speed, and secure cryptographic scheme that has the added advantage of being immune to side-channel attacks. In our article, we have shown that the performance of this scheme is superior in certain aspects to that of the A5/1 system used in global system for mobile (GSM) systems. The parallel architecture employed in this scheme makes it suitable to use in systems where the data-processing operations have to be carried out in real time. Residue number systems (RNS) based on Chinese remainder theorem (CRT) permits the representation of large integers in terms of combinations of smaller ones. The set of all CRT number system representation of an integer from 0 to M-1 with component wise modular addition and multiplication constitutes a direct sum of smaller commutative rings. An encryption and decryption algorithm based on the properties of direct sum of smaller rings offers distinct advantages over decimal or fixed radix arithmetic. We have utilized the representation of integers using CRT to successfully design additive, multiplicative, and affine stream cipher systems. The use of number system based on CRT allows speeding up the encryption/decryption algorithms, reduces the time complexity, and provides immunity to side-channel, algebraic, and known plain text attacks. In this article, the characteristics of additive, multiplicative, and affine stream cipher systems based on CRT number system representation have been studied and analyzed.
NSF funding advice
Authors: Wing Jeannette M. , Reed Daniel 
Published: April 2010

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

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Jeannette M. Wing shares useful suggestions for department heads.
Daniel Reed discusses the importance of synergy among computing specialists and generalists.
Immunogenic Tumor Cell Death for Optimal Anticancer Therapy: The Calreticulin Exposure Pathway
Authors: Zitvogel Laurence , Kepp Oliver , Senovilla Laura , Menger Laurie , Chaput Nathalie , Kroemer Guido 
Published: April 2010

Abstract
In response to some chemotherapeutic agents such as anthracyclines and oxaliplatin, cancer cells undergo immunogenic apoptosis, meaning that their corpses are engulfed by dendritic cells and that tumor cell antigens are presented to tumor-specific CD8+ T cells, which then control residual tumor cells. One of the peculiarities of immunogenic apoptosis is the early cell surface exposure of calreticulin (CRT), a protein that usually resides in the lumen of the endoplasmic reticulum (ER). When elicited by anthracyclines or oxaliplatin, the CRT exposure pathway is activated by pre-apoptotic ER stress and the phosphorylation of the eukaryotic translation initiation factor eIF2α by the kinase PERK, followed by caspase-8-mediated proteolysis of the ER-sessile protein BAP31, activation of the pro-apoptotic proteins Bax and Bak, anterograde transport of CRT from the ER to the Golgi apparatus and exocytosis of CRT-containing vesicles, finally resulting in CRT translocation onto the plasma membrane surface. Interruption of this complex pathway abolishes CRT exposure, annihilates the immunogenicity of apoptosis, and reduces the immune response elicited by anticancer chemotherapies. We speculate that human cancers that are incapable of activating the CRT exposure pathway are refractory to the immune-mediated component of anticancer therapies. Clin Cancer Res; 16(12); 3100–4. ©2010 AACR.
Storminess and Environmental Changes in the Mediterranean Central Area
Authors: Diodato Nazzareno , Bellocchi Gianni 
Published: April 2010

Abstract
Earth ecosystems are not static, and they respond to environmental changes, particularly climatic and anthropogenic. Precipitation varying in its extremeness, with shifts to greater or lesser intensity of individual storms and/or to change in the length and frequency of wet and dry periods, can adversely affect both urban and rural ecosystems. Here, the authors review long-term precipitation records of the central Mediterranean area and employ a Web geographical information system (GIS)-based analytical approach to compare current rainfall impact with historical data on different spatial and temporal scales. Autumn (September–November) was recognized as the most hazardous season that marks the evidence of a changing climate, with a shift toward more intense rainfalls in recent times. In the first decade of the third millennium, areas of peninsular and insular Italy have been especially affected by extreme rains. A focus was put on the island of Sicily, where extraordinary rain events occurred in September 2009, discussed in the context of upcoming trends and climate histories. An improved knowledge and understanding of the scale at which changes on extremes occur is essential for dealing with the forthcoming challenges regarding soil and water conservation practices. The characteristics of changes in natural rainfall, its role on terrestrial ecosystems, and its effect on surface water erosion dynamics are discussed. It is argued that understanding these issues are major priorities for future research to promote a better understanding of the Earth interaction with water resources and related hydrological issues.
Transmission electron microscopy (TEM) of Earth and planetary materials: A review
Authors: Lee M. R. 
Published: April 2010

AbstractUsing high intensity beams of fast electrons, the transmission electron microscope (TEM) and scanning transmission electron microscope (STEM) enable comprehensive characterization of rocks and minerals at micrometre to sub-nanometre scales. This review outlines the ways in which samples of Earth and planetary materials can be rendered sufficiently thin for TEM and STEM work, and highlights the significant advances in site-specific preparation enabled by the focused ion beam (FIB) technique. Descriptions of the various modes of TEM and STEM imaging, electron diffraction and X-ray and electron spectroscopy are outlined, with an emphasis on new technologies that are of particular relevance to geoscientists. These include atomic-resolution Z-contrast imaging by high-angle annular dark-field STEM, electron crystallography by precession electron diffraction, spectrum mapping using X-rays and electrons, chemical imaging by energy-filtered TEM and true atomic-resolution imaging with the new generation of aberration-corrected microscopes. Despite the sophistication of modern instruments, the spatial resolution of imaging, diffraction and X-ray and electron spectroscopy work on many natural materials is likely to remain limited by structural and chemical damage to the thin samples during TEM and STEM.
Demicheleite-(I), BiSI, a new mineral from La Fossa Crater, Vulcano, Aeolian Islands, Italy
Authors: Demartin F. , Gramaccioli C. M. , Campostrini I. 
Published: April 2010

AbstractDemicheleite-(I), ideally BiSI, is the iodine-dominant analogue of demicheleite-(Br) and demicheleite-(Cl). It was found in an active medium-temperature intracrateric fumarole at La Fossa crater, Vulcano Island, Aeolian archipelago, Sicily, Italy. The mineral is the first bismuth sulphoiodide so far discovered in a wholly natural environment, and corresponds to the already known synthetic compound. It occurs as acicular to stout, translucent crystals up to 0.25 mm long in an altered pyroclastic breccia, together with demicheleite-(Br), bismoclite, bismuthinite, godovikovite, panichiite, aiolosite, brontesite, adranosite and other new phases under study. The colour is dark red to black, the lustre submetallic. The unit cell is orthorhombic, space groupPnam, witha= 8.4501(7) Å,b= 10.1470(9) Å ,c= 4.1389(4) Å ,V= 354.88(4) Å3, andZ= 4. The crystal habit is prismatic, with the main forms {110} and {111} inferred from analogy with demicheleite-(Br). Twinning was not observed. The strongest 6 lines in the X-ray powder diffraction pattern [dobs.(Å) (I/I0) (hkl)] are: 6.490 (100) (110); 4.346 (94) (120); 3.896 (90) (210); 2.709 (60) (310); 2.161 (38) (330); 3.243 (22) (220). The chemical analysis obtained by WDS electron microprobe gave: Bi 58.32, S 9.43, I 23.69, Br 5.66, Cl 1.01, totalling 98.11 wt.%, corresponding to an empirical formula (based on 3 a.p.f.u.) of: Bi0.97S1.03(I0.65Br0.25Cl0.10)Σ1.00. The unit-cell data are close to those of the synthetic compound, whose crystal structure is already known. The calculated density is 6.411 g cm–3.
Heklaite, KNaSiF6, a new fumarolic mineral from Hekla volcano, Iceland
Authors: Garavelli A. , Balić-Žunić T. , Mitolo D. , Acquafredda P. , Leonardsen E. , Jakobsson S. P. 
Published: April 2010

AbstractHeklaite, with the ideal formula KNaSiF6, was found among fumarolic encrustations collected in 1992 on the Hekla volcano, Iceland. Heklaite forms a fine-grained mass of micron- to sub-micron-sized crystals intimately associated with malladrite, hieratite and ralstonite. The mineral is colourless, transparent, non-fluorescent, has a vitreous lustre and a white streak. The calculated density is 2.69 g cm–3. An SEM-EDS quantitative chemical analysis shows the following range of concentrations (wt.%): Na 11.61–12.74 (average 11.98), K 17.02–18.97 (average 18.29), Si 13.48 –14.17 (average 13.91), F 54.88–56.19 (average 55.66). The empirical chemical formula, calculated on the basis of 9 a.p.f.u., is Na1.07K0.96Si1.01F5.97. X-ray powder diffraction indicates that heklaite is orthorhombic, space groupPnma, with the following unit-cell parameters:a= 9.3387(7) Å,b= 5.5032(4) Å,c= 9.7957(8) Å ,V= 503.43(7) Å3,Z= 4. The eight strongest reflections in the powder diffraction pattern [din Å (I/I0) (hkl)] are: 4.33 (53) (102); 4.26 (56) (111); 3.40 (49) (112); 3.37 (47) (202); 3.34 (100) (211); 2.251 (27) (303); 2.050 (52) (123); 2.016 (29) (321). On the basis of chemical analyses and X-ray data, heklaite corresponds to the synthetic compound KNaSiF6. The name is for the type locality, the Hekla volcano, Iceland.
The early publication of new mineral names: new procedures for the release of new mineral names and publication
Authors: Mills S.J. 
Published: April 2010

AbstractNew procedures are put in place in order to facilitate the dissemination of new mineral names into the public arena. Authors will get the opportunity to select whether the Commission will release the new mineral name upon successful approval in the Commission's monthly newsletter, which will be published in Mineralogical Magazine. Authors are also entitled to have the name not released until final publication, i.e. to retain the status quo. This will enable citations to be made using the new mineral name until the full description is published. Modifications to the existing rules, on the two-year time frame for new mineral publication, are also outlined.
The crystal structure and compositional range of mckinstryite
Authors: Kolitsch U. 
Published: April 2010

AbstractThe previously unknown crystal structure of mckinstryite, originally described as Ag1.18Cu0.82S or (Ag,Cu)2S, was solved and refined using single-crystal X-ray diffractometer data collected from a sample from the Clara mine, Black Forest (Mo-Kα radiation, CCD area detector, R1(F) = 3.85%). Mckinstryite has the refined formula Ag4.92Cu3.08S4 or Ag1.23Cu0.77S (idealized Ag5Cu3S4 or Ag1.25Cu0.75S) and crystallizes in space group Pnma (no. 62), with a = 14.047(3) Å, b = 7.805(2) Å , c = 15.691(3) Å, V = 1720.3(7) Å3, Z = 8. The structure contains five Ag, six Cu and eight S sites in the asymmetric unit. One of the Ag sites shows minor Cu-for-Ag substitution. The topology is based on flat, interrupted (010) layers of Cu and S atoms (all atoms on y = 0.25), in which the Cu atoms show triangular or two-coordination to S (interrupted {6,3} tiling). These layers alternate with uneven layers consisting of Ag atoms showing irregular three- to two-coordination to S. Some fairly short Ag–Cu contact distances (2.781–2.884 Å) strongly indicate that metal-metal interaction plays an important role in mckinstryite. The topology is related to that of stromeyerite (∼AgCuS) which contains complete flat layers of Cu atoms triangularly coordinated to S atoms, alternating with layers of loosely packed Ag atoms.A critical evaluation of literature data on the chemical composition and unit-cell parameters of mckinstryite confirms the presence of a small compositional range of mckinstryite which extends approximately from Ag1.18Cu0.82S to Ag1.25Cu0.75S, with the presently studied sample being fairly Agrich. The accurate limits of this range at ambient temperature are still to be determined.
Senescence induction in human fibroblasts and hematopoietic progenitors by leukemogenic fusion proteins
Authors: Wajapeyee Narendra , Wang Shu-Zong , Serra Ryan W. , Solomon Peter D. , Nagarajan Arvindhan , Zhu Xiaochun , Green Michael R. 
Published: April 2010

Abstract
Hematologic malignancies are typically associated with leukemogenic fusion proteins, which are required to maintain the oncogenic state. Previous studies have shown that certain oncogenes that promote solid tumors, such as RAS and BRAF, can induce senescence in primary cells, which is thought to provide a barrier to tumorigenesis. In these cases, the activated oncogene elicits a DNA damage response (DDR), which is essential for the senescence program. Here we show that 3 leukemogenic fusion proteins, BCR-ABL, CBFB-MYH11, and RUNX1-ETO, can induce senescence in primary fibroblasts and hematopoietic progenitors. Unexpectedly, we find that senescence induction by BCR-ABL and CBFB-MYH11 occurs through a DDR-independent pathway, whereas RUNX1-ETO induces senescence in a DDR-dependent manner. All 3 fusion proteins activate the p38 MAPK pathway, which is required for senescence induction. Our results reveal diverse pathways for oncogene-induced senescence and further suggest that leukemias harbor genetic or epigenetic alterations that inactivate senescence induction genes.
Prognostic impact of IDH2 mutations in cytogenetically normal acute myeloid leukemia
Authors: Thol Felicitas , Damm Frederik , Wagner Katharina , Göhring Gudrun , Schlegelberger Brigitte , Hoelzer Dieter , Lübbert Michael , Heit Wolfgang , Kanz Lothar , Schlimok Günter , Raghavachar Aruna , Fiedler Walter , Kirchner Hartmut , Heil Gerhard , Heuser Michael , Krauter Jürgen , Ganser Arnold 
Published: April 2010

Abstract
Mutations in the nicotinamide adenine dinucleotide phosphate+–dependent isocitrate dehydrogenase gene 2 (IDH2) have recently been found in patients with acute myeloid leukemia (AML) as well as in patients with leukemic transformation of myeloproliferative neoplasms. We analyzed 272 adult patients with cytogenetically normal AML (CN-AML) for the presence of IDH2 mutations in codons R140 and R172. IDH2 mutations of amino acid 140 or 172 could be identified in 12.1% of CN-AML patients, with the majority of mutations (90%) occurring at position R140. The incidence of IDH2 mutations in AML patients with aberrant karyotypes (n = 130) was significantly lower (3.8%, P = .006). IDH2 mutations were mutually exclusive with mutations in IDH1. IDH2 mutation status alone or in combination with IDH1 mutations had no impact on response to therapy, overall survival, and relapse-free survival in patients with CN-AML. In conclusion, IDH2 mutations are frequently found in CN-AML, but in our analysis these mutations did not influence treatment outcome. This study was registered at www.clinicaltrials.gov as #NCT00209833.