bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bariosincosite, a new hydrated barium vanadium phosphate, from the Spring
Creek Mine, South Australia
Authors: Pring A. , Kolitsch U. , Birch W. D. , Beyer B. D. , Elliott P. , Ayyappan P. , Ramanan A. 
Published: November 2006

Abstract
Bariosincosite is a new barium vanadium phosphate hydrate from the Spring
Creek Mine, near Wilmington, South Australia. The new mineral occurs as irregular
clusters of pale green, very thin platey crystals up to 250 µm across and 2 to 5
µm thick. The tetragonal crystals are tabular on {001} and the other form present
is {100}. Associated with bariosincosite are quartz, cuprite, native copper,
fluorapatite, whitlockite, baryte and springcreekite,
BaV33+
(PO4)2(OH,H2O)6.
Bariosincosite appears to have formed under supergene or low-temperature
late-stage hydrothermal conditions. Electron microprobe analysis yielded: BaO
23.20; SrO 4.19; CaO 0.36; VO2 31.55;
Fe2O3 0.20;
Al2O3 0.50;
P2O5 28.15; H2O
13.93 (calculated). These data give an empirical formula of
(Ba0.77Sr0.20Ca0.03)∑1.00[(V0.964+
Al0.03Fe0.013+)∑1.00O(PO4)]2·4H2O,
calculated on the basis of two P atoms. The simplified formula is
Ba(V4+OPO4)2·4H2O.
The mineral is transparent with a very pale green streak, a vitreous lustre and an
estimated Mohs hardness of 3. The strongest lines in the X-ray powder pattern are
[dobs
(Iobs)
(hkl)] 6.414 (20) (110, 002); 5.748 (70) (111);
4.552 (30) (112, 200); 3.198 (20) (220, 004); 3.100 (100) (203, 221); 2.847 (40)
(222, 114); 2.786 (80) (311); 2.368 (30) (313, 115); and 2.017 (100) (420, 332,
116). These data were indexed on a tetragonal cell, with
a = 9.031(6), c =
12.755(8) Å and V = 1040(1) Å3;
the space group is probably P4/n or
P4/nmm. For Z = 4 and
using the empirical formula, the calculated density is 3.306
gm/cm3. Bariosincosite is uniaxial negative with ω =
1.721(2) and ε = 1.715(2) (white light); pleochroism is weak from colourless (E)
to pale green (O), absorption O > E. The mineral is named for the relationship
to sincosite,
Ca(V4+OPO4)2·4H2O.
‘Coutinite’, ‘coutinhite’ and ‘neodymite’ discredited as identical to
lanthanite-(La) and/or lanthanite-(Nd)
Authors: Atencio D. 
Published: November 2006

Abstract
The names ‘coutinite’ [= lanthanite-(Nd)], ‘coutinhite’ [= lanthanite-(La)],
and ‘neodymite' [= lanthanite-(Nd) or lanthanite-(La)], do not follow the rules of
nomenclature for rare earth minerals. These names were introduced without
International Mineralogical Association (IMA) approval and are now formally
discarded (Nomenclature Proposal 98-B) by the Commission on New Minerals and
Mineral Names (CNMMN) of the IMA.
Pumpellyite from the oceanic crust, DSDP/ODP Hole 504B
Authors: Ishizuka H. 
Published: November 2006

Abstract
Pumpellyite has been found in doleritic basalt of a sheeted dyke complex
drilled from 2072.1 m below sea floor in DSDP/ODP Hole 504B, south of the Costa
Rica Rift, eastern Pacific. It occurs as fine-grained crystal aggregates
accompanied by albite, chlorite and chalcopyrite, which partially replace a
plagioclase phenocryst (An85–88) that is also associated with
primary magnetite. Chemical compositions of the pumpellyite vary antithetically in
relation to Fe* and Al as well as Fe* and Mg, indicating the dominant substitution
of Fe3+ by Al with the minor substitution of
Fe2+ by Mg. Such compositional variations overlap with
those of prehnite-pumpellyite facies rocks dredged from other oceanic ridges and
intra-oceanic arcs, and those of similar facies rocks from ophiolites, but are
aluminous compared with those of zeolite facies metabasites in ophiolites. These
observations suggest that the breakdown of the plagioclase phenocryst and
magnetite in the presence of a Cu- and S-bearing fluid phase led to the formation
of pumpellyite + albite + chlorite + chalcopyrite during oceanic ridge
hydrothermal alteration.
Disorder and compositional variation in the lillianite homologous series
Authors: Pring A. , Jercher M. , Makovicky E. 
Published: November 2006

AbstractHigh resolution transmission electron microscopy studies on the lillianite group minerals from the Ivigtut cryolite deposit, Ivigtut, South Greenland revealed the existence of disordered intergrowths of lillianite/gustavite-like blocks (N− 4) and heyrovskyite-like (N= 7) structural blocks. One disorder sequence is examined in detail, which gave an average homologue number N = 4.92 corresponding to a composition of Pb3.922xBi2·xAgxS6.92with x ≈ 1.2. An Axial Next-Nearest Neighour Ising model was used to follow the fluctuations in the average homologue numberNacross the crystal. This yielded compositional fluctuations of the order of 70–170 Å over a 1800 Å region of the crystal, with a 202 Å lamella of ordered vikingite. Trends in the randomness of the gustavite-vikingite intergrowth were evaluated and the dominant slab sequence was found to be 4,4,4,7 and 4,4,7,7, suggesting that some longer period homologues may be stable. A number of defects were noted in which changes in slab widths were accommodated. The origin of these partially ordered/disordered lillianite homologues is discussed.
Fe-Li micas: a new approach to the substitution series
Authors: Shihua Sun , Jie Yu 
Published: November 2006

Abstract
Over the last 50 years many definitions of element substitution series have
been proposed for describing natural Fe-Li micas with complex chemical
compositions. In order to compare these definitions and ascertain their
reliability, a new geometric frame composed of ideal mica points, mica joins
(segments), substitution vectors and substitution planes is constructed to express
the entire substitution system of ideal Fe-Al-Li micas. The frame is built in
composition space with the coordinate system (0; Si, AlVI
AlIV, Fe2+, Li,
□VI, K), but has a 3-dimensional analogue, i.e. a visual
image.
Using this frame, it has been proved that there are only five possible types
of replacement for definitions of Fe-Li micas, and that all possible types have
been suggested except the AlIV-constant. Furthermore, it has
been proved that the main point in different definitions is that the replacement
of Li by Fe2+ needs to be balanced with
AlIV, AlVI, or
□VI. In order to solve this problem, a set of formulae
determining spatial relations between geometric elements in the frame is
suggested. With these formulae, the abstract frame is suggested to be a datum
system used to ascertain quantitatively the reliability of definition of natural
Fe-Li micas.
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model
Authors: Xia Kai , Dong Dong , Han Jing-Dong J 
Published: November 2006

Abstract

Background
Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking.

Results
By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs.

Conclusion
IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at http://hanlab.genetics.ac.cn/IntNetDB.htm. Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer.
Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism
Authors: Wang Zhijun , Xiang Li , Shao Junjie , Węgrzyn Alicja , Węgrzyn Grzegorz 
Published: November 2006

Abstract

Background
Although understanding of physiological interactions between plasmid DNA and its host is important for vector design and host optimization in many biotechnological applications, to our knowledge, global studies on plasmid-host interactions have not been performed to date even for well-characterized plasmids.

Results

Escherichia coli cells, either devoid of plasmid DNA or bearing plasmid pOri1 (with a single ColE1 replication origin) or plasmid pOri2 (with double ColE1 replication origins), were cultured in a chemostat. We used a combination of metabolic flux analysis, DNA microarray and enzyme activity analysis methods to explore differences in the metabolism between these strains. We found that the presence of plasmids significantly influenced various metabolic pathways in the host cells, e.g. glycolysis, the tricarboxylic acid (TCA) cycle and the pentose phosphate (PP) pathway. Expression of rpiA, a gene coding for ribose-5-phosphate isomerase A, was considerably decreased in E. coli carrying a high copy number plasmid relative to E. coli carrying a low copy number plasmid and plasmid-free E. coli. The rpiA gene was cloned into an expression vector to construct plasmid pETrpiA. Following induction of pETrpiA-bearing E. coli, which harbored either pOri1 or pOri2, with isopropyl-β-D-thiogalactopyranoside (IPTG), the copy number of pOri1 and pOri2 was sigificantly higher than that measured in a host devoid of pETrpiA.

Conclusion
The presence of plasmids can significantly influence some metabolic pathways in the host cell. We believe that the results of detailed metabolic analysis may be useful in optimizing host strains, vectors and cultivation conditions for various biotechnological purposes.
Highly Variable Year‐to‐Year Prevalence of Anaplasma phagocytophilum in Ixodes ricinus Ticks in Northeastern Poland: A 4‐Year Follow‐up
Authors: GRZESZCZUK ANNA , STAŃCZAK JOANNA 
Published: November 2006

Abstract:
Anaplasma phagocytophilum is transmitted mainly by Ixodes ricinus ticks in Europe. We followed‐up A. phagocytophilum infection rate in I. ricinus in three selected collection sites in northeastern Poland during a four‐year period. Overall infection rate was 14.1% (208/1474) with highest infection rate among females (36.8% verses males 8.2% and nymphs 0.9%). We noted a very big year‐to‐year variation of infection prevalence in each collection cite every year reflecting changeable granulocytic anaplasmosis risk for humans and animals.
Focusing on Host–Vector–Pathogen Interactions for Vaccine Development
Authors: FUENTE JOSÉde la , AYOUBI PATRICIA , BLOUIN EDMOUR F. , ALMAZÁN CONSUELO , NARANJO VICTORIA , KOCAN KATHERINE M. 
Published: November 2006

Abstract:
Anaplasma marginale and A. phagocytophylum are intracellular rickettsiae that cause bovine anaplasmosis and human granulocytic anaplasmosis, respectively. The ultimate vaccine for the control of anaplasmosis would be one that reduces infection and transmission of the pathogen by ticks. Effective vaccines for control of anaplasmosis are not available despite attempts using different approaches, such as attenuated strains, infected erythrocyte and tick cell‐derived purified antigens, and recombinant pathogen and tick‐derived proteins. Three lines of functional analyses were conducted by our laboratory to characterize host–tick–Anaplasma interactions to discover potential vaccine candidate antigens to control tick infestations and the infection and transmission of Anaplasma spp.: (1) characterization of A. marginale adhesins involved in infection and transmission of the pathogen, (2) global expression analysis of genes differentially expressed in HL‐60 human promyelocytic cells in response to infection with A. phagocytophilum, and (3) identification and characterization of tick‐protective antigens by expression library immunization (ELI) and analysis of expressed sequence tags (EST) in a mouse model of tick infestations and by RNA interference in ticks. These experiments have resulted in the characterization of the A. marginale MSP1a as an adhesin for bovine erythrocytes and tick cells, providing support for its use as candidate vaccine antigen for the control of bovine . Microarray analysis of genes differentially expressed in human cells infected with A. phagocytophilum identified key molecules involved in pathogen infection and multiplication. The screening for tick‐protective antigens resulted in vaccine candidates reducing tick infestation, molting, and oviposition and affecting Anaplasma infection levels in ticks.
Cytokine Gene Expression by Peripheral Blood Leukocytes in Dogs Experimentally Infected with a New Virulent Strain of Ehrlichia canis
Authors: UNVER AHMET , HUANG HAIBIN , RIKIHISA YASUKO 
Published: November 2006

Abstract:
Ehrlichia canis (E. canis) is a lipopolysaccharide (LPS)‐deficient obligatory intracellular bacterium that causes canine monocytic ehrlichiosis, a chronic febrile disease accompanied with hematological abnormality. This study analyzed temporal expression levels of IL‐1β, IL‐2, IL‐6, IL‐8, IFN‐γ, and TNF‐α mRNA by peripheral blood leukocytes from dogs experimentally infected with a new virulent strain of E. canis by using real‐time RT‐PCR. Relative levels of IL‐1β and IL‐8 transcripts normalized by the β‐actin transcript levels, were significantly upregulated, whereas those of TNF‐α and IFN‐γ transcripts were only weakly upregulated in all three infected dogs, starting from 2 days up to 52 days post inoculation. The expressions of IL‐2 and IL‐6 genes were extremely low compared with the positive control (ConA‐stimulated canine peripheral blood leukocytes). This study showed that E. canis can induce chronic expression of a subset of proinflammatory cytokine genes: balance, timing, and duration of these cytokine generations may contribute to the progression of canine ehrlichiosis.
Diagnosis of Coxiella burnetii Pericarditis Using a Systematic Prescription Kit in Case of Pericardial Effusion
Authors: LEVY P.Y. , THUNY F. , HABIB G. , BONNET J.L. , DJIANE P. , RAOULT D. 
Published: November 2006

Abstract:
Coxiella burnetii, regarded as a potential agent of pericarditis, wa found to be responsible for almost 5% of the cases of idiopathic pericardial effusion reported in this series. Diagnosis was aided by use of a systematic kit described in this paper.
Changes in Attentional Performance of Children and Young Adults With Localized Primary Brain Tumors After Conformal Radiation Therapy
Authors: Kiehna Erin N. , Mulhern Raymond K. , Li Chenghong , Xiong Xiaoping , Merchant Thomas E. 
Published: November 2006

Purpose To prospectively assess the impact of conformal radiation therapy (CRT) and demographic and clinical variables on four measures of attention in pediatric and young adult patients with localized primary brain tumors. Patients and Methods We prospectively evaluated 120 patients with primary brain tumors, ages 2 to 24.4 years (median, 9.2 years). Evaluations were done using the computerized Conners' Continuous Performance Test (CCPT). We analyzed errors of omission (inattentiveness), errors of commission (impulsivity), reaction time, and an overall index of performance before CRT, weekly during CRT, and serially up to 60 months after the start of CRT. Results Before CRT, patients exhibited mild inattentiveness. During CRT, impulsivity decreased significantly (P = .002). After CRT, inattentiveness increased significantly (P = .03), and global attention disorders were associated with craniopharyngioma (P < .0001), supratentorial tumors (P = .008), optic pathway and diencephalic tumors (P = .012), and subtotal resection of the tumor (P = .010). Conclusion Brain tumors and their treatment impair sustained attention and reaction time. A decline in impulsivity and relative stability of the other CCPT scores over the course of CRT demonstrated the absence of early radiation-related cognitive sequelae. Local tumor effects, initial surgical intervention, and focal irradiation of central structures contribute to long-lasting attentional problems in pediatric and young adult patients.
Identification of Tumor-Specific Molecular Signatures in Intracranial Ependymoma and Association With Clinical Characteristics
Authors: Modena Piergiorgio , Lualdi Elena , Facchinetti Federica , Veltman Joris , Reid James F. , Minardi Simone , Janssen Irene , Giangaspero Felice , Forni Marco , Finocchiaro Gaetano , Genitori Lorenzo , Giordano Flavio , Riccardi Riccardo , Schoenmakers Eric F.P.M. , Massimino Maura , Sozzi Gabriella 
Published: November 2006

Purpose To delineate clinically relevant molecular signatures of intracranial ependymoma. Materials and Methods We analyzed 24 primary intracranial ependymomas. For genomic profiling, microarray-based comparative genomic hybridization (CGH) was used and results were validated by fluorescent in situ hybridization and loss of heterozygosity mapping. We performed gene expression profiling using microarrays, real-time quantitative reverse transcriptase polymerase chain reaction, and methylation analysis of selected genes. We applied class comparison analyses to compare both genomic and expression profiling data with clinical characteristics. Results A variable number of genomic imbalances were detected by array CGH, revealing multiple regions of recurrent gain (including 2q23, 7p21, 12p, 13q21.1, and 20p12) and loss (including 5q31, 6q26, 7q36, 15q21.1, 16q24, 17p13.3, 19p13.2, and 22q13.3). An ependymoma-specific gene expression signature was characterized by the concurrent abnormal expression of developmental and differentiation pathways, including NOTCH and sonic hedgehog signaling. We identified specific differentially imbalanced genomic clones and gene expression signatures significantly associated with tumor location, patient age at disease onset, and retrospective risk for relapse. Integrated genomic and expression profiling allowed us to identify genes of which the expression is deregulated in intracranial ependymoma, such as overexpression of the putative proto-oncogene YAP1 (located at 11q22) and downregulation of the SULT4A1 gene (at 22q13.3). Conclusion The present exploratory molecular profiling study allowed us to refine previously reported intervals of genomic imbalance, to identify novel restricted regions of gain and loss, and to identify molecular signatures correlating with various clinical variables. Validation of these results on independent data sets represents the next step before translation into the clinical setting.
Plasma Osteopontin Is an Independent Prognostic Marker for Head and Neck Cancers
Authors: Petrik David , Lavori Philip W. , Cao Hongbin , Zhu Yonghua , Wong Priscilla , Christofferson Erin , Kaplan Michael J. , Pinto Harlan A. , Sutphin Patrick , Koong Albert C. , Giaccia Amato J. , Le Quynh-Thu 
Published: November 2006

PurposeTo confirm the relationship between plasma osteopontin (OPN) levels and treatment outcomes in head and neck squamous cell carcinoma (HNSCC) patients in an expanded study.Patients and MethodsOne hundred forty patients with newly diagnosed HNSCC were enrolled onto this study, 54 previously reported and 86 new patients. Pretreatment plasma OPN levels were assessed in all patients by an enzyme-linked immunosorbent assay method. OPN levels were correlated to treatment outcomes in the new group of patients. Detailed analyses were also performed on the relationship between OPN and tumor control rate, event-free survival (EFS), and postrelapse survival for the entire group.ResultsUsing a previously defined cut off point of 450 ng/mL, there was a significant correlation between OPN and freedom-from-relapse (P = .047), overall survival (P = .019), and EFS (P = .023) in the new, independent patient cohort (n = 86). Sequence of event analyses using the entire group (N = 140) revealed that OPN was an independent prognostic factor for initial tumor control, EFS in those who have achieved tumor control, and postrelapse survival.ConclusionIn this expanded study, we were able to replicate the prognostic significance of OPN using a predefined cut off point in an independent patient group and demonstrated that plasma OPN is an independent prognostic marker for HNSCC.
Phase II Study of Consolidation Paclitaxel After Concurrent Chemoradiation in Poor-Risk Stage III Non–Small-Cell Lung Cancer: SWOG S9712
Authors: Davies Angela M. , Chansky Kari , Lau Derick H.M. , Leigh Bryan R. , Gaspar Laurie E. , Weiss Geoffrey R. , Wozniak Antoinette J. , Crowley John J. , Gandara David R. 
Published: November 2006

Purpose A previous Southwest Oncology Group (SWOG) study (S9429) demonstrated efficacy and tolerability of concurrent chemoradiotherapy in poor-risk stage III non–small-cell lung cancer (NSCLC). This study evaluated adding consolidation paclitaxel after chemoradiotherapy for a similar patient cohort. Patients and Methods Patients with histologically/cytologically determined stage III NSCLC were eligible based on performance status (PS) 2 and either low albumin or weight loss more than 10%, poor pulmonary function, or comorbidities precluding cisplatin use. Treatment was carboplatin 200 mg/m2 days 1, 3, 29, and 31, and etoposide 50 mg/m2 days 1 through 4, and 29 to 32. Beginning day 1, thoracic radiation was delivered at 1.8 Gy in 25 fractions plus 16-Gy boost (total dose, 61 Gy). Patients without disease progression received paclitaxel 175 mg/m2 every 21days for three cycles. Results Characteristics of 87 eligible patients were age 51 to 82 years; 57% PS 0 to 1, 43% PS 2; and 51% stage IIIA, 49% stage IIIB. Toxicities of concurrent chemoradiotherapy included grade 3 esophagitis (7%) and grade 3/4 neutropenia (43%). Fifty-four assessable patients received paclitaxel consolidation. Four treatment-related deaths occurred during chemoradiotherapy and four occurred during consolidation. Overall response rate was 53%. Median progression free- and overall survival were 6.1 and 10.2 months, respectively. One- and 2-year survival rates were 43% and 25%. Conclusion Compared with a previous SWOG trial in a similar patient population, the addition of consolidation paclitaxel after chemoradiotherapy resulted in increased toxicity without a survival advantage. More PS 2 patients (43% v 18%) enrolled onto S9712, which may explain increased toxicity and lack of benefit. The optimal chemoradiotherapy approach for poor-risk patients remains to be defined.