bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coiraite, (Pb,Sn2+)12.5As3Fe2+Sn4+5S28: a franckeite-type new mineral species from Jujuy Province, NW Argentina
Authors: Paar W. H. , Moëlo Y. , Mozgova N. N. , Organova N. I. , Stanley C. J. , Roberts A. C. , Culetto F. J. , Effenberger H. S. , Topa D. , Putz H. , Sureda R. J. , de Brodtkorb M. K. 
Published: March 2009

AbstractCoiraite, ideally (Pb,Sn2+)12.5As3Fe2+Sn4+S28, occurs as an economically important tin ore in the large Ag-Sn-Zn polymetallic Pirquitas deposit, Jujuy Province, NW-Argentina. The new mineral species is the As derivative of franckeite and belongs to the cylindrite group of complex Pb sulphosalts with incommensurate composite-layered structures. It is a primary mineral, frequently found in colloform textures, and formed from hydrothermal solutions at low temperature. Associated minerals are franckeite, cylindrite, pyrite-marcasite, as well as minor amounts of hocartite, Ag-rich rhodostannite. arsenopyrite and galena. Laminae of coiraite consist of extremely thin bent platy crystals up to 50 urn long. Electron microprobe analysis(n =31) gave an empirical formula Pb11.21As2.99Ag0.13Fe1.10Sn6.13S28.0close to the ideal formula (Pb11.3Sn2+1.2)Σ=12.5As3Fe2+Sn4+S28. Coiraite has two monoclinic sub-cells,Q(pseudotetragonal) andH(pseudohexagonal).Q: a5.84(1) Å,b5.86(1) Å, c 17.32(1) Å, β 94.14(1)°, F 590.05(3) Å3, Z = 4,a:b:c =0.997:1:2.955; H (orthogonal setting):a6.28(1) Å,b3.66(1) Å, c 17.33(1) Å, β 91.46(1)°,V398.01(6) Å3, Z= 2, a∶b∶c =1.716∶1∶4.735. The strongest Debye-Scherrer camera X-ray powder-diffraction lines[din Å,(I), (hkl)]are: 5.78, (20),(QandH003); 4.34, (40),(Q004); 3.46, (30),(Qand H 005); 3.339, (20),(Q104); 2.876, (100),(Qand H 006); 2.068, (60),(Q220).
Mushroom elbaite from the Kat Chay mine, Momeik, near Mogok, Myanmar: II. Zoning and crystal growth
Authors: Lussier A. J. , Hawthorne F. C. , Herwig S. , Abdu Y. , Aguiar P. M. , Michaelis V. K. , Kroeker S. 
Published: March 2009

AbstractA variety of mushroom tourmaline from the Kat Chay mine, Momeik, near Mogok, Shan state, Myanmar, consists of a black-to-grey single-crystal core from which a single prismatic crystal reaches to the edge of the mushroom, forming a slight protuberance. The rest of the mushroom (∼50% by volume) consists of extremely acicular sub-parallel crystals that diverge toward the edge of the mushroom. The acicular crystals are dominantly colourless to white, with a continuous black zone (2 mm across) near the edge, and pale pink outside the black zone. The composition varies from ∼Na0.75Ca0.05(Li0.80Al0.70Fe1.10.Mn0.30Ti0.10)Al6Si6(B03)3O18(OH)3(OH,F) at the base of the mushroom to ∼Na0.60Ca0.06(Li1.00Al1.98Fe0.02)Al6(Si5.35B0.65)(BO3)3O18(OH)3(OH,F) close to the edge at the top of the mushroom. The principal substitutions are: (1) YLi + YAl -> yFe* + yFe* and (2) TB + yAl -> Si + yFe*, but there are five other minor substitutions that are also operative. There are six significant compositional discontinuities at textural boundaries in the mushroom, suggesting that the changes in habit are driven in part by changes in external variables such as T and P, plus possible involvement of new fluid phases.
Costimulatory ligand CD70 allows induction of CD8+ T-cell immunity by immature dendritic cells in a vaccination setting
Authors: Keller Anna M. , Xiao Yanling , Peperzak Victor , Naik Shalin H. , Borst Jannie 
Published: March 2009

Abstract
The use of dendritic cells (DCs) as anticancer vaccines holds promise for therapy but requires optimization. We have explored the potential of costimulatory ligand CD70 to boost the capacity of DCs to evoke effective CD8+ T-cell immunity. We show that immature conventional DCs, when endowed with CD70 expression by transgenesis, are converted from a tolerogenic state into an immunogenic state. Adoptively transferred CD70-expressing immature DCs could prime CD8+ T cells, by CD27, to become tumor-eradicating cytolytic effectors and memory cells with a capacity for robust secondary expansion. The CD8+ T-cell response, including memory programming, was independent of CD4+ T-cell help, because the transferred immature DCs were loaded with major histocompatibility complex class I–restricted peptide only. Without CD70 expression, the DCs generated abortive clonal expansion, dysfunctional antitumor responses, and no CD8+ T-cell memory. CD70-expressing CD8+ DCs were the primary subset responsible for CD8+ T-cell priming and performed comparably to fully matured DCs. These data highlight the importance of CD27/CD70 interactions at the T-cell/DC interface and indicate that CD70 should be considered in the design of DC vaccination strategies.
Ectopic HOXB4 overcomes the inhibitory effect of tumor necrosis factor-α on Fanconi anemia hematopoietic stem and progenitor cells
Authors: Milsom Michael D. , Schiedlmeier Bernhard , Bailey Jeff , Kim Mi-Ok , Li Dandan , Jansen Michael , Ali Abdullah Mahmood , Kirby Michelle , Baum Christopher , Fairbairn Leslie J. , Williams David A. 
Published: March 2009

AbstractEctopic delivery of HOXB4 elicits the expansion of engrafting hematopoietic stem cells (HSCs). We hypothesized that inhibition of tumor necrosis factor-α (TNF-α) signaling may be central to the self-renewal signature of HOXB4. Because HSCs derived from Fanconi anemia (FA) knockout mice are hypersensitive to TNF-α, we studied Fancc−/− HSCs to determine the physiologic effects of HOXB4 on TNF-α sensitivity and the relationship of these effects to the engraftment defect of FA HSCs. Overexpression of HOXB4 reversed the in vitro hypersensitivity to TNF-α of Fancc−/− HSCs and progenitors (P) and partially rescued the engraftment defect of these cells. Coexpression of HOXB4 and the correcting FA-C protein resulted in full correction compared with wild-type (WT) HSCs. Ectopic expression of HOXB4 resulted in a reduction in both apoptosis and reactive oxygen species in Fancc−/− but not WT HSC/P. HOXB4 overexpression was also associated with a significant reduction in surface expression of TNF-α receptors on Fancc−/− HSC/P. Finally, enhanced engraftment was seen even when HOXB4 was expressed in a time-limited fashion during in vivo reconstitution. Thus, the HOXB4 engraftment signature may be related to its effects on TNF-α signaling, and this pathway may be a molecular target for timed pharmacologic manipulation of HSC during reconstitution.
Cutaneous lymphoma incidence patterns in the United States: a population-based study of 3884 cases
Authors: Bradford Porcia T. , Devesa Susan S. , Anderson William F. , Toro Jorge R. 
Published: March 2009

Abstract
There have been no prior large population-based studies focusing on cutaneous lymphomas (CL) in the United States. Using the Surveillance, Epidemiology and End Results (SEER) program data, we analyzed age-adjusted CL incidence rates (IRs) and survival rates by sex and race/ethnicity. There were 3884 CLs diagnosed during 2001-2005. Cutaneous T-cell lymphomas (CTCLs) accounted for 71% (age-adjusted incidence rate [IR] = 7.7/1 000 000 person-years), whereas cutaneous B-cell lymphomas(CBCLs) accounted for 29% (IR = 3.1/1 000 000 person-years). Males had a statistically significant higher IR of CL than females (14.0 vs 8.2/1 000 000 person-years, respectively; male-female IR ratio [M/F IRR] = 1.72; P < .001). CL IRs were highest among blacks and non-Hispanic whites (both 11.5/1 000 000 person-years), followed by Hispanic whites (7.9) and Asian/Pacific Islanders (7.1). The CTCL IR was highest among blacks (10.0/1 000 000 person-years), whereas the CBCL IR was highest among non-Hispanic whites (3.5). Over the past 25 years, the CL IR increased from 5.0/1 000 000 person-years during 1980-1982 to 14.3 during 2001-2003. During 2004-2005, the CL IR was 12.7. This recent apparent change could be incomplete case ascertainment or potential leveling off of IRs. CLs rates vary markedly by race and sex, supporting the notion that they represent distinct disease entities.
A family of splice variants of CstF-64 expressed in vertebrate nervous systems
Authors: Shankarling Ganesh S , Coates Penelope W , Dass Brinda , MacDonald Clinton C 
Published: March 2009

Abstract

Background
Alternative splicing and polyadenylation are important mechanisms for creating the proteomic diversity necessary for the nervous system to fulfill its specialized functions. The contribution of alternative splicing to proteomic diversity in the nervous system has been well documented, whereas the role of alternative polyadenylation in this process is less well understood. Since the CstF-64 polyadenylation protein is known to be an important regulator of tissue-specific polyadenylation, we examined its expression in brain and other organs.

Results
We discovered several closely related splice variants of CstF-64 – collectively called βCstF-64 – that could potentially contribute to proteomic diversity in the nervous system. The βCstF-64 splice variants are found predominantly in the brains of several vertebrate species including mice and humans. The major βCstF-64 variant mRNA is generated by inclusion of two alternate exons (that we call exons 8.1 and 8.2) found between exons 8 and 9 of the CstF-64 gene, and contains an additional 147 nucleotides, encoding 49 additional amino acids. Some variants of βCstF-64 contain only the first alternate exon (exon 8.1) while other variants contain both alternate exons (8.1 and 8.2). In mice, the predominant form of βCstF-64 also contains a deletion of 78 nucleotides from exon 9, although that variant is not seen in any other species examined, including rats. Immunoblot and 2D-PAGE analyses of mouse nuclear extracts indicate that a protein corresponding to βCstF-64 is expressed in brain at approximately equal levels to CstF-64. Since βCstF-64 splice variant family members were found in the brains of all vertebrate species examined (including turtles and fish), this suggests that βCstF-64 has an evolutionarily conserved function in these animals. βCstF-64 was present in both pre- and post-natal mice and in different regions of the nervous system, suggesting an important role for βCstF-64 in neural gene expression throughout development. Finally, experiments in representative cell lines suggest that βCstF-64 is expressed in neurons but not glia.

Conclusion
This is the first report of a family of splice variants encoding a key polyadenylation protein that is expressed in a nervous system-specific manner. We propose that βCstF-64 contributes to proteomic diversity by regulating alternative polyadenylation of neural mRNAs.
Prevalence of pathogenetic MC4R mutations in Italian children with early Onset obesity, tall stature and familial history of obesity
Authors: Santoro Nicola , Cirillo Grazia , Xiang Zhimin , Tanas Rita , Greggio Nella , Morino Giuseppe , Iughetti Lorenzo , Vottero Alessandra , Salvatoni Alessandro , Di Pietro Mario , Balsamo Antonio , Crinò Antonino , Grandone Anna , Haskell-Luevano Carrie , Perrone Laura , del Giudice Emanuele Miraglia 
Published: March 2009

Abstract

Background
Melanocortin-4-receptor (MC4R) mutations represent the most frequent genetic cause of non-syndromic early onset obesity. Children carrying MC4R mutations seem to show a particular phenotype characterized by early onset, severe obesity and high stature. To verify whether MC4R mutations are associated with this particular phenotype in the Italian pediatric population, we decided to screen the MC4R gene in a group of obese children selected on the basis of their phenotype.

Methods
To perform this study, a multicentric approach was designed. Particularly, to be enrolled in the study subjects needed to meet the following criteria: Body mass index ≥ 3 deviation scores according to age and sex, familiar history of obesity (at least one parent obese), obesity onset before the 10 years old, height ≥ 2 deviation scores. The coding region of MC4R gene was screened in 240 obese children (mean age 8.3 ± 3.1, mean BMI 30.8 ± 5.4) and in 200 controls (mean age 8.1 ± 2.8; mean BMI 14.2 ± 2.5).

Results
Three mutations have been found in five obese children. The S127L (C380T), found in three unrelated children, had been described and functionally characterized previously. The Q307X (C919T) and the Y332H (T994C) mutations were found in two patients. Functional studies showed that only Q307X impaired protein function.

Conclusion
The low prevalence of MC4R mutations (1.6%) in this group of obese children selected according to the obesity degree, the tall stature and the family history of obesity was similar to the prevalence observed in previous screenings performed in obese adults and in not phenotypically selected obese children.
Better estimation of protein-DNA interaction parameters improve prediction of functional sites
Authors: Nagaraj Vijayalakshmi H , O'Flanagan Ruadhan A , Sengupta Anirvan M 
Published: March 2009

AbstractBackgroundCharacterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method designed to produce many such sequences.ResultsWe analyzed low stringency SELEX data forE. coliCatabolic Activator Protein (CAP), and we show here that appropriate quantitative analysis improves our ability to predictin vitroaffinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Rouletet al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones) in theE. coligenome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay) and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation) trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related speciesS. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites.ConclusionWe think that training binding site detection algorithms on datasets from binding assays lead to better prediction. The improvements in accuracy came from the unbiased nature of the SELEX dataset rather than from the number of sites available. We believe that with progress in short-read sequencing technology, one could use SELEX methods to characterize binding affinities of many low specificity transcription factors.
Connexins: a myriad of functions extending beyond assembly of gap junction channels
Authors: Dbouk Hashem A , Mroue Rana M , El-Sabban Marwan E , Talhouk Rabih S 
Published: March 2009

Abstract
Connexins constitute a large family of trans-membrane proteins that allow intercellular communication and the transfer of ions and small signaling molecules between cells. Recent studies have revealed complex translational and post-translational mechanisms that regulate connexin synthesis, maturation, membrane transport and degradation that in turn modulate gap junction intercellular communication. With the growing myriad of connexin interacting proteins, including cytoskeletal elements, junctional proteins, and enzymes, gap junctions are now perceived, not only as channels between neighboring cells, but as signaling complexes that regulate cell function and transformation. Connexins have also been shown to form functional hemichannels and have roles altogether independent of channel functions, where they exert their effects on proliferation and other aspects of life and death of the cell through mostly-undefined mechanisms. This review provides an updated overview of current knowledge of connexins and their interacting proteins, and it describes connexin modulation in disease and tumorigenesis.
A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acid
Authors: DeFraia Christopher T , Schmelz Eric A , Mou Zhonglin 
Published: March 2009

AbstractBackgroundSalicylic acid (SA) is an important signalling molecule in plant defenses against biotrophic pathogens. It is also involved in several other processes such as heat production, flowering, and germination. SA exists in the plant as free SA and as an inert glucose conjugate (salicylic acid 2-O-β-D-glucoside or SAG). Recently, Huanget al. developed a bacterial biosensor that responds to free SA but not SAG, designated asAcinetobactersp. ADPWH_lux. In this paper we describe an improved methodology forAcinetobactersp. ADPWH_lux-based free SA quantification, enabling high-throughput analysis, and present an approach for the quantification of SAG from crude plant extracts.ResultsOn the basis of the original biosensor-based method, we optimized extraction and quantification. SAG content was determined by treating crude extracts with β-glucosidase, then measuring the released free SA with the biosensor. β-glucosidase treatment released more SA in acetate buffer extract than in Luria-Bertani (LB) extract, while enzymatic hydrolysis in either solution released more free SA than acid hydrolysis. The biosensor-based method detected higher amounts of SA in pathogen-infected plants than did a GC/MS-based method. SA quantification of control and pathogen-treated wild-type andsid2(SA induction-deficient) plants demonstrated the efficacy of the method described. Using the methods detailed here, we were able to detect as little as 0.28 μg SA/g FW. Samples typically had a standard deviation of up to 25% of the mean.ConclusionThe ability ofAcinetobactersp. ADPWH_luxto detect SA in a complex mixture, combined with the enzymatic hydrolysis of SAG in crude extract, allowed the development of a simple, rapid, and inexpensive method to simultaneously measure free and glucose-conjugated SA. This approach is amenable to a high-throughput format, which would further reduce the cost and time required for biosensor-based SA quantification. Possible applications of this approach include characterization of enzymes involved in SA metabolism, analysis of temporal changes in SA levels, and isolation of mutants with aberrant SA accumulation.
The Neuroscience Peer Review Consortium
Authors: Saper Clifford B , Maunsell John HR 
Published: March 2009

AbstractAs the Neuroscience Peer Review Consortium (NPRC) ends its first year, it is worth looking back to see how the experiment has worked.In order to encourage dissemination of the details outlined in this Editorial, it will also be published in other journals in the Neuroscience Peer Review Consortium.
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation
Authors: Barrett Christian L , Herrgard Markus J , Palsson Bernhard 
Published: March 2009

Abstract

Background
Metabolism and its regulation constitute a large fraction of the molecular activity within cells. The control of cellular metabolic state is mediated by numerous molecular mechanisms, which in effect position the metabolic network flux state at specific locations within a mathematically-definable steady-state flux space. Post-translational regulation constitutes a large class of these mechanisms, and decades of research indicate that achieving a network flux state through post-translational metabolic regulation is both a complex and complicated regulatory problem. No analysis method for the objective, top-down assessment of such regulation problems in large biochemical networks has been presented and demonstrated.

Results
We show that the use of Monte Carlo sampling of the steady-state flux space of a cell-scale metabolic system in conjunction with Principal Component Analysis and eigenvector rotation results in a low-dimensional and biochemically interpretable decomposition of the steady flux states of the system. This decomposition comes in the form of a low number of small reaction sets whose flux variability accounts for nearly all of the flux variability in the entire system. This result indicates an underlying simplicity and implies that the regulation of a relatively low number of reaction sets can essentially determine the flux state of the entire network in the given growth environment.

Conclusion
We demonstrate how our top-down analysis of networks can be used to determine key regulatory requirements independent of specific parameters and mechanisms. Our approach complements the reductionist approach to elucidation of regulatory mechanisms and facilitates the development of our understanding of global regulatory strategies in biological networks.
Conventional intramuscular sedatives versus ziprasidone for severe agitation in adolescents: case-control study
Authors: Jangro William C , Preval Horacio , Southard Robert , Klotz Steven G , Francis Andrew 
Published: March 2009

Abstract

Objective
The objective of this study was to compare intramuscular (IM) ziprasidone to conventional IM medications (haloperidol combined with lorazepam) for the treatment of severe agitation in adolescents (age 12–17).

Methods
We retrospectively identified consecutive severe agitation episodes (defined as requiring physical restraint) in adolescents treated with either IM ziprasidone or conventional IM agents in a psychiatric emergency room. For ziprasidone, the dosage was 20 mg for 23 episodes and 10 mg for 5 episodes. For 24 episodes treated with combined haloperidol and lorazepam, the dosages were 4.8 ± 0.3 SEM mg and 1.9 ± 0.4 mg respectively. Outcomes were the duration of restraint and need for adjunctive "rescue" medications within 60 minutes. These outcomes were decided prior to reviewing any records.

Results
No difference was found in restraint duration (ziprasidone, N = 28, 55 ± 5 minutes; haloperidol with lorazepam N = 24, 65 ± 7 minutes, P = NS). Use of "rescue" medications did not differ between the two groups. No changes in blood pressure were found, but pulse decreased 8.3 ± 2.4 for haloperidol with lorazepam and 8.9 ± 4.24 for ziprasidone (P = NS). No instances of excessive sedation or extra-pyramidal symptoms were documented.

Conclusion
In this study, IM ziprasidone appeared effective, well tolerated, and similar in clinical profile to combined conventional IM medications for treating severe agitation in adolescents. Given the reportedly favorable acute side effect profile of parenteral atypical agents, they may provide an alternative to conventional antipsychotics for treating acute agitation in both adult and adolescent populations. Future randomized, controlled studies are needed.