bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted deletion of α-adducin results in absent β- and γ-adducin, compensated hemolytic anemia, and lethal hydrocephalus in mice
Authors: Robledo Raymond F. , Ciciotte Steven L. , Gwynn Babette , Sahr Kenneth E. , Gilligan Diana M. , Mohandas Narla , Peters Luanne L. 
Published: August 2008

AbstractIn the red blood cell (RBC), adducin is present primarily as tetramers of α- and β-subunits at spectrin-actin junctions, or junctional complexes. Mouse RBCs also contain small amounts of γ-adducin. Platelets contain α- and γ-adducin only. Adducin functions as a barbed-end actin capping protein to regulate actin filament length and recruits spectrin to the ends of actin filaments. To further define adducin's role in vivo, we generated α-adducin knockout mice. α-Adducin is absent in all tissues examined in homozygous null mice. In RBCs, β- and γ-adducin are also absent, indicating that α-adducin is the limiting subunit in tetramer formation at the spectrin-actin junction. Similarly, γ-adducin is absent in α-null platelets. α-Adducin–null mice display compensated hemolytic anemia with features characteristic of RBCs in hereditary spherocytosis (HS), including spherocytes with significant loss of surface area, decreased mean corpuscular volume (MCV), cell dehydration, and increased osmotic fragility. Platelets maintain their normal discoid shape, and bleeding times are normal. α-Adducin–null mice show growth retardation at birth and throughout adulthood. Approximately 50% develop lethal communicating hydrocephalus with striking dilation of the lateral, third, and fourth ventricles. These data indicate that adducin plays a role in RBC membrane stability and in cerebrospinal fluid homeostasis.
Integration of relational and hierarchical network information for protein function prediction
Authors: Jiang Xiaoyu , Nariai Naoki , Steffen Martin , Kasif Simon , Kolaczyk Eric D 
Published: August 2008

Abstract

Background
In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.

Results
We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.

Conclusion
A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.
Differential screening identifies transcripts with depot-dependent expression in white adipose tissues
Authors: Wu Yu , Kim Ji Young , Zhou Shengli , Smas Cynthia M 
Published: August 2008

Abstract

Background
The co-morbidities of obesity are tied to location of excess fat in the intra-abdominal as compared to subcutaneous white adipose tissue (WAT) depot. Genes distinctly expressed in WAT depots may impart depot-dependent physiological functions. To identify such genes, we prepared subtractive cDNA libraries from murine subcutaneous (SC) or intra-abdominal epididymal (EP) white adipocytes.

Results
Differential screening and qPCR validation identified 7 transcripts with 2.5-fold or greater enrichment in EP vs. SC adipocytes. Boc, a component of the hedgehog signaling pathway demonstrated highest enrichment (~12-fold) in EP adipocytes. We also identified a dramatic enrichment in SC adipocytes vs. EP adipocytes and in SC WAT vs. EP WAT for transcript(s) for the major urinary proteins (Mups), small secreted proteins with pheromone functions that are members of the lipocalin family. Expression of Boc and Mup transcript was further assessed in murine tissues, adipogenesis models, and obesity. qPCR analysis reveals that EP WAT is a major site of expression of Boc transcript. Furthermore, Boc transcript expression decreased in obese EP WAT with a concomitant upregulation of Boc transcript in the obese SC WAT depot. Assessment of the Boc binding partner Cdon in adipose tissue and cell fractions thereof, revealed transcript expression similar to Boc; suggestive of a role for the Boc-Cdon axis in WAT depot function. Mup transcripts were predominantly expressed in liver and in the SC and RP WAT depots and increased several thousand-fold during differentiation of primary murine preadipocytes to adipocytes. Mup transcripts were also markedly reduced in SC WAT and liver of ob/ob genetically obese mice compared to wild type.

Conclusion
Further assessment of WAT depot-enriched transcripts may uncover distinctions in WAT depot gene expression that illuminate the physiological impact of regional adiposity.
Survey of extrachromosomal circular DNA derived from plant satellite repeats
Authors: Navrátilová Alice , Koblížková Andrea , Macas Jiří 
Published: August 2008

Abstract

Background
Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.

Results
We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.

Conclusion
This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.
Results of emergency Hartmann's operation for obstructive or perforated left-sided colorectal cancer
Authors: Charbonnet Pierre , Gervaz Pascal , Andres Axel , Bucher Pascal , Konrad Béatrice , Morel Philippe 
Published: August 2008

Abstract

Background
Up to 15% of colorectal cancer (CRC) patients present with obstructive or perforated tumours, and require emergency surgery. The Hartmann's procedure (HP) provides the opportunity to achieve a potentially curative (R0) resection, while minimizing surgical trauma in poor-risk patients. The aim of this study was to assess the surgical (operative mortality), and oncological (long-term survival after curative resection) results of emergency HP for obstructive or perforated left-sided CRC.

Methods
A retrospective review of 50 patients who underwent emergency HP for perforated/obstructive CRC in our institution between 1995 and 2006.

Results
Median age of patients was 75 (range 22–95) years and the indications for HP were obstruction (32) and perforation (18 patients). Operative mortality and morbidity were 8% and 26% respectively. 35 patients (70%) were operated with a curative intent; in this group, overall 1-, 3- and 5-year survival rates were 80%, 54% and 40%. In univariate analysis, the presence of lymph node metastases was associated with poor 5-year survival (62% [Stage II] vs. 27% [Stage III], log-rank test, p = 0.02). Eleven patients (22%) had their operation reversed with a median delay of 225 (range 94–390) days. In this subgroup, two patients died from distant metastases, but there were no instances of loco-regional recurrence.

Conclusion
Hartmann's operation remains a good option to palliate symptoms in 30% of patients with left-sided CRC who are not candidates to a curative resection. For those who have a curative resection, the oncological outcome is acceptable, especially stage II patients, who appear to benefit the most from this surgical strategy.
Does preoperative analysis of intrahepatic venous anastomoses improve the surgeon's intraoperative decision making? Pilot data from a case report
Authors: Fischer Lars , Schoebinger Max , Neumann Jan-Oliver , Müller Sascha , Meinzer Hans-Peter , Büchler Markus W , Schmied Bruno M 
Published: August 2008

Abstract

Background
Three-dimensional (3D) visualization is thought to improve the anatomical understanding of clinicians, thus improving patient safety.

Case presentation
A 58-year-old male was admitted to our hospital in April 2007 with a suspected metastasis of a sigmoid cancer in the Couinaud segment (CS) 7. The anatomical situation of this patient was analyzed using both a CT scan and 3D images. The initial CT scan revealed that the proximal part of the middle hepatic vein was completely missing and the metastasis in the CS 7 was closely attached to the right hepatic vein. After analyzing additional 3D images, it became clear that due to the close proximity of metastasis and right hepatic vein, the resection of the right hepatic vein was inevitable. Based on this 3D analysis, it was decided to perform a right-sided hemihepatectomy. In this case report, 3D visualization resulted in a faster and clearer understanding of the unique anatomical situation in a patient with complicated liver anatomy than transversal CT images.

Conclusion
The here presented data shows for the first time 3D visualization of intravenous anastomoses in the human liver. The information offered by 3D visualization is not redundant but rather serves as a true source of additional information, indicating the potential benefit of 3D visualization in surgical operation planning.
Predicting acoustic orientation in complex real-world environments
Authors: Mhatre Natasha , Balakrishnan Rohini 
Published: August 2008

SUMMARYAnimals have to accomplish several tasks in their lifetime, such as finding food and mates and avoiding predators. Animals that locate these using sound need to detect, recognize and localize appropriate acoustic objects in their environment, typically in noisy, non-ideal conditions. Quantitative models attempting to explain or predict animal behaviour should be able to accurately simulate behaviour in such complex, real-world conditions. Female crickets locate potential mates in choruses of simultaneously calling males. In the present study, we have tested field cricket acoustic orientation behaviour in complex acoustic conditions in the field and also successfully predicted female orientation and paths under these conditions using a simulation model based on auditory physiology. Such simulation models can provide powerful tools to predict and dissect patterns of behaviour in complex, natural environments.
Influence of Mn(III) availability on the phase transformation from layered buserite to tunnel-structured todorokite
Authors: Cui Haojie , Liu Xiangwen , Tan Wenfeng , Feng Xionghan , Liu Fan , Ruan Huada Daniel 
Published: August 2008

AbstractTodorokite is a common Mn oxide mineral in terrestrial and ocean-floor environments, and it is commonly synthesized from layered Na-buserite. Pyrophosphate, which is known to form strong complexes with Mn(III) at a pH range of 1–8, was added to a suspension of Na-buserite in order to sequester the available Mn(III) in Na-buserite. No Mn(III)-pyrophosphate complex was formed in solution at pH 10, and the treated Na-buserites were converted completely to todorokite. Significant transformation reductions were observed when Na-buserite was treated with pyrophosphate solution at pH 7. The presence of Mn(III) within the MnO6 octahedral sheets of Na-buserite is critical for the transformation from layered buserite to tunnel-structured todorokite at atmospheric pressure. At lower pH, two effects are combined to reduce the amount of Mn(III) in the layers: (1) the complexing power of pyrophosphate is increased; and (2) the transformation from Na-buserite to H-birnessite, which is concomitant with the migration of Mn(III) from layers to the interlayer, and the partial disproportionation of Mn(III). The results showed that Mn(III) played a key role in the transformation of layered Na-buserite to tunnel-structured todorokite at atmospheric pressure.
Preferred orientation of mineral grains in sample mounts for quantitative XRD measurements: How random are powder samples?
Authors: Kleeberg Reinhard , Monecke Thomas , Hillier Stephen 
Published: August 2008

AbstractThe degree of preferred orientation of mineral grains in powder X-ray diffraction (XRD) samples prepared by standard techniques has been evaluated by means of a correction model implemented in the Rietveld program, BGMN. It is demonstrated that neither front- nor side-loading of mineral powders obtained by wet grinding in a McCrone micronizing mill yield powder mounts with randomly oriented particles. Despite fine grinding, the primary sizes and shapes of mineral grains contained in multi-phase samples influence the degree of preferred orientation in XRD powder mounts. Two minerals, both of platy habit, were found to show different degrees of preferred orientation in front- and side-loaded samples. In contrast to these methods of sample preparation, the spray-drying technique yielded perfect randomness of the particles. The experiments on artificial mineral mixtures demonstrate that the model applied can effectively correct for preferred orientation allowing reliable Rietveld quantitative phase analysis of moderately textured samples prepared by standard techniques.
Role of Microbial Fe(III) Reduction and Solution Chemistry in Aggregation and Settling of Suspended Particles in the Mississippi River Delta Plain, Louisiana, USA
Authors: Jaisi Deb P. , Ji Shanshan , Dong Hailiang , Blake Ruth E. , Eberl Dennis D. , Kim Jinwook 
Published: August 2008

AbstractRiver-dominated delta areas are primary sites of active biogeochemical cycling, with productivity enhanced by terrestrial inputs of nutrients. Particle aggregation in these areas primarily controls the deposition of suspended particles, yet factors that control particle aggregation and resulting sedimentation in these environments are poorly understood. This study was designed to investigate the role of microbial Fe(III) reduction and solution chemistry in aggregation of suspended particles in the Mississippi Delta. Three representative sites along the salinity gradient were selected and sediments were collected from the sediment-water interface. Based on quantitative mineralogical analyses 88–89 wt.% of all minerals in the sediments are clays, mainly smectite and illite. Consumption of SO42−\$\end{document} and the formation of H2S and pyrite during microbial Fe(III) reduction of the non-sterile sediments by Shewanella putrefaciens CN32 in artificial pore water (APW) media suggest simultaneous sulfate and Fe(III) reduction activity. The pHPZNPC of the sediments was ⩽3.5 and their zeta potentials at the sediment-water interface pH (6.9–7.3) varied from −35 to −45 mV, suggesting that both edges and faces of clay particles have negative surface charge. Therefore, high concentrations of cations in pore water are expected to be a predominant factor in particle aggregation consistent with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Experiments on aggregation of different types of sediments in the same APW composition revealed that the sediment with low zeta potential had a high rate of aggregation. Similarly, addition of external Fe(II) (i.e. not derived from sediments) was normally found to enhance particle aggregation and deposition in all sediments, probably resulting from a decrease in surface potential of particles due to specific Fe(II) sorption. Scanning and transmission electron microscopy (SEM, TEM) images showed predominant face-to-face clay aggregation in native sediments and composite mixtures of biopolymer, bacteria, and clay minerals in the bioreduced sediments. However, a clear need remains for additional information on the conditions, if any, that favor the development of anoxia in deep- and bottom-water bodies supporting Fe(III) reduction and resulting in particle aggregation and sedimentation.
The trapping of B from water by exfoliated and functionalized vermiculite
Authors: Kehal Mohamed , Reinert Laurence , Maurin David , Bantignies Jean-Louis , Ohashi Fumihiko , Mennour Ammar , Duclaux Laurent 
Published: August 2008

AbstractMicron-grade natural vermiculite was modified by several physical and chemical treatments in order to increase the adsorption capacity of this material for B. A thermal exfoliation (T = 600°C) of pristine material, a chemical exfoliation through reaction with hydrogen peroxide (H2O2 35%), or grafting of a specific B complexant (i.e. N-methyl-D-glucamine: NMDG) led to an increase in the uptake of B at low initial concentrations of the aqueous solutions ([B] ≈ 5 mg L−1). The more efficient material is the NMDG-grafted clay, for which the adsorption uptake is four times greater than that of raw vermiculite, and reaches 0.04 mmol g−1. For all modified materials, the effect of the pH on B adsorption and the adsorption kinetics were studied and compared to raw vermiculite. Adsorption isotherms were also plotted and fitted well with the Freundlich equation.
XRD, FTIR, and thermal analysis of bauxite ore-processing waste (red mud) exchanged with heavy metals
Authors: Castaldi Paola , Silvetti Margherita , Santona Laura , Enzo Stefano , Melis Pietro 
Published: August 2008

AbstractThe present work shows the results of X-ray diffraction (XRD), Fourier transform infrared (FTIR), and thermal analysis of untreated (RMnt) and acid-treated red mud (RMa), a bauxite ore-processing waste, exchanged with Pb2+, Cd2+, and Zn2+ cations. These studies were performed in order to investigate the changes in the sorbent structure caused by the exchange with metals of different ionic radii.The XRD pattern of RMnt, analyzed according to the Rietveld method, showed a mixture of eight different phases. However, just three phases made up 78 wt.% of the RMnt: cancrinite (33 wt.%), hematite (29 wt.%), and sodalite (16 wt.%). X-ray diffraction patterns of RMnt exchanged with Pb2+ and Cd2+ cations revealed two additional phases, namely hydrocerussite [Pb3(CO3)2(OH)2 (10 wt.%))] and octavite [CdCO3 (8 wt.%)].These two phases probably originated from the carbonate precipitation processes which were due to the decarbonation of cancrinite. Hydrocerussite and octavite were not found in the case of acid-treated red mud samples.In the FTIR spectra, the introduction of cations caused a distinct shift to higher wavenumbers in the peak at ∼1100 cm−1, which is attributed to the asymmetric stretch of Si-O-Al. This effect may be associated with the Pb2+, Cd2+, and Zn2+ adsorbed by the red muds which caused a deformation of the initial structure.Thermal analysis data of the red mud samples were obtained by thermogravimetric/differential thermogravimetric analysis, and these methods were employed to evaluate the desorption behavior of water and to clarify the thermal stability of the chemical phases of the different red mud samples. The loss of metal-bound water in the red mud samples was found to depend on the size of non-framework cations and water loss consistently followed the order: Zn2+>Cd2+>Pb2+.
Improved Granulocyte Colony-Stimulating Factor Mobilization of Hemopoietic Progenitors Using Cytokine Combinations in Primates
Authors: Larsen Stephen R. , Chng Keefe , Battah Fiona , Martiniello-Wilks Rosetta , Rasko John E.J. 
Published: August 2008

AbstractPeripheral blood stem cells (PBSCs), usually mobilized with granulocyte colony-stimulating factor (G-CSF) alone or in combination with chemotherapy, are the preferred source of cells for hemopoietic stem cell transplantation. Up to 25% of otherwise eligible transplant recipients fail to harvest adequate PBSCs. Therefore it is important to investigate existing and novel reagents to improve PBSC mobilization. Because of marked interindividual variation in humans, we developed a robust nonhuman primate model that allows the direct comparison of the efficacy of two PBSC mobilization regimens within the same animal. Using this model, we compared pegylated G-CSF (pegG-CSF) with standard G-CSF and compared the combination of G-CSF and pegylated megakaryocyte growth and development factor (pegMGDF) with G-CSF plus stem cell factor (SCF) by measuring the levels of CD34+ cells, colony-forming cells (CFCs), and SCID repopulating cells (SRCs) before and after cytokine administration. Mobilization of CD34+ cells, CFCs and SRCs using pegG-CSF achieved similar levels to those resulting from 5 days of standard G-CSF. The combination of G-CSF+pegMGDF mobilized progenitors to levels similar to G-CSF+SCF but greater than standard G-CSF for CD34+ cells and CFC. This first direct comparison of PBSC mobilization in individual primates demonstrates that peg-G-CSF is equivalent to daily G-CSF and that the addition of pegMGDF to G-CSF improves mobilization. In light of the development of new thrombopoietin agonists, these data offer the potential for improved stem cell mobilization strategies.Disclosure of potential conflicts of interest is found at the end of this article.