bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A‐Minor Motif Enhances in vitro Antibacterial Activity
Authors: Kondo Jiro , Pachamuthu Kandasamy , François Boris , Szychowski Janek , Hanessian Stephen , Westhof Eric 
Published: August 2007

AbstractThe crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the γ‐amino‐α‐hydroxybutyryl (L‐haba) group at position N1 of ring II (2‐DOS ring), and an ether chain with an O‐phenethylaminoethyl group at position C2′′ of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A‐minor interaction between two bulged‐out adenines from the A site and the codon–anticodon stem of the mRNA–tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the “on” state with two bulged out adenines, and 2) a new binding mode of 1 to an A‐minor motif which stabilizes complex formation between the ribosome and the mRNA–tRNA complex regardless of whether the codon–anticodon stem is of the cognate or near‐cognate type.
The impact of hepatitis B viral load on recurrence after complete necrosis in patients with hepatocellular carcinoma who receive transarterial chemolipiodolization
Authors: Jang Jeong Won , Choi Jong Young , Bae Si Hyun , Yoon Seung Kew , Woo Hyun Young , Chang U Im , Kim Chang Wook , Nam Soon Woo , Cho Se Hyun , Yang Jin Mo , Lee Chang Don 
Published: August 2007

AbstractBACKGROUND.Hepatocellular carcinoma (HCC) has a high tendency for recurrence after radical treatment. Apart from tumor and liver function parameters, little is known about the role of hepatitis B virus (HBV) factors in the recurrence of HCC. The objective of this study was to identify the potential relation between viral load and HCC recurrence in patients undergoing transarterial chemolipiodolization.METHODS.This was a cohort study of 62 consecutive patients who had HBV‐related HCC and achieved complete necrosis with transarterial chemolipiodolization. Risk factors, including viral load for posttreatment recurrence, were analyzed.RESULTS.Overall, 32 of 62 patients (51.6%) developed a recurrence during the study period (7.2–37.5 months). Multivariate analysis established Child‐Pugh Class B (P = .014), multiple tumors (P = .013), and high viral load (HBV DNA levels >105 copies/mL) at complete necrosis (P = .001) as independent risk factors for recurrence. On both univariate and multivariate analyses, high viral load at the time of complete necrosis was identified as the strongest factor for recurrence; moreover, its statistically significant effects still were observed even when conducting the analyses separately for both local recurrence (P = .018) and distant recurrence (P = .009).CONCLUSIONS.Among individuals who underwent transarterial chemolipiodolization, high HBV viral load at complete necrosis was among the most important risk factors for posttreatment recurrence, irrespective of the locational pattern of recurrence. The current findings underscored the need for future work that tests the applicability of antiviral therapy to reduce the risk of HCC recurrence in this setting. Cancer 2007. © 2007 American Cancer Society.
Features at presentation predict children with acute lymphoblastic leukemia at low risk for tumor lysis syndrome
Authors: Truong Tony H. , Beyene Joseph , Hitzler Johann , Abla Oussama , Maloney Anne Marie , Weitzman Sheila , Sung Lillian 
Published: August 2007

AbstractBACKGROUND.Tumor lysis syndrome (TLS) is a well‐recognized complication of acute lymphoblastic leukemia (ALL). The ability to predict children at differing risk of TLS would be an early step toward risk‐based approaches. The objectives of the current study were 1) to describe the prevalence and predictors of TLS in childhood ALL and 2) to develop a sensitive prediction rule to identify patients at lower risk of TLS.METHODS.Health records of children aged ≤18 years who were diagnosed with ALL between 1998 and 2004 were reviewed. TLS was defined by the presence of ≥2 laboratory abnormalities occurring in the time frame of interest. Predictors of TLS were determined using univariate and multiple logistic regression analyses.RESULTS.Among 328 patients, 23% met criteria for TLS. Factors predictive of TLS were male sex (odds ratio [OR], 1.8; P = .041), age ≥10 years (OR, 4.5; P < .0001), splenomegaly (OR, 3.3; P < .0001), mediastinal mass (OR, 12.2; P < .0001), T‐cell phenotype (OR, 8.2; P < .0001), central nervous system involvement (OR, 2.8; P = .026), lactate dehydrogenase ≥2000 U/L (OR, 7.6; P < .0001), and white blood count (WBC) ≥20 × 109/L (OR, 4.7; P < .0001). Among variables that were available at presentation, multiple regression analysis identified age ≥10 years, splenomegaly, mediastinal mass, and initial WBC ≥20 × 109/L as independent predictors of TLS. When all 4 of those predictors were absent at presentation (n = 114 patients), the negative predictive value of developing TLS was 97%, with a sensitivity of 95%.CONCLUSIONS.Clinical and laboratory features at the time of presentation identified a group of children with ALL at low risk for TLS that may benefit from a risk‐stratified approach directed at reduced TLS monitoring and prophylaxis. Cancer 2007. © 2007 American Cancer Society.
Differential expression of peroxisomal matrix and membrane proteins during postnatal development of mouse brain
Authors: Ahlemeyer Barbara , Neubert Inge , Kovacs Werner J. , Baumgart‐Vogt Eveline 
Published: August 2007

AbstractIn peroxisomal biogenesis disorders, serious neurological abnormalities can be observed in the patients and the respective knockout mouse models. As a prerequisite for a better understanding of the relationship between the absence of peroxisomes and the observed neuropathology, knowledge of the regional and cell‐type specific distribution of peroxisomal proteins in mouse brain is necessary. Therefore, we investigated the expression of distinct peroxins, peroxisomal membrane and matrix proteins (e.g. Pex5p, Pex14p, Pex13p, PMP70, catalase, peroxisomal thiolase, Acox1, “SKL”‐PTS1 proteins) by indirect immunofluorescence 1) in primary cultures of the medial neocortex, hippocampus, and cerebellum of newborn mice and 2) in paraffin sections of mouse brain of different ages (newborn–adult). Quantitative analysis revealed a comparable abundance (number/μm2) of peroxisomes in cultured neurons and astrocytes of all three brain regions. In contrast, catalase immunoreactivity was higher in cultured astrocytes than in neurons. In mouse brain tissue, the abundance of peroxisomes decreased by half during postnatal development, also exhibiting prominent differences between distinct brain regions and cell types. Catalase protein levels in neuronal peroxisomes, however, decreased much more strongly in the neocortex, CA1–3 areas of the hippocampus, dentate gyrus, cerebellar nuclei, and cerebellar cortex but remained high in Bergmann glia and other astrocytes, epithelial cells of the choroid plexus, and ependyma. Similar age‐dependent changes were found for thiolase and Acox1 protein levels. Developmental changes were confirmed by Western blot analysis using enriched peroxisomal and cytosolic fractions of the brain tissue as well as by measurement of catalase activity. J. Comp. Neurol. 505:1–17, 2007. © 2007 Wiley‐Liss, Inc.
Regenerating optic axons restore topography after incomplete optic nerve injury
Authors: Dunlop Sarah A. , Tee Lisa B.G. , Goossens Michel A.L. , Stirling R. Victoria , Hool Livia , Rodger Jenny , Beazley L.D. 
Published: August 2007

AbstractFollowing complete optic nerve injury in a lizard, Ctenophorus ornatus, retinal ganglion cell (RGC) axons regenerate but fail to restore retinotectal topography unless animals are trained on a visual task (Beazley et al. [ 1997] J Comp Neurol 370:105–120, [2003] J Neurotrauma 20:1263–1270). Here we show that incomplete injury, which leaves some RGC axons intact, restores normal topography. Strict RGC axon topography allowed us to preserve RGC axons on one side of the nerve (projecting to medial tectum) while lesioning those on the other side (projecting to lateral tectum). Topography and response properties for both RGC axon populations were assessed electrophysiologically. The majority of intact RGC axons retained appropriate topography in medial tectum and had normal, consistently brisk, reliable responses. Regenerate RGC axons fell into two classes: those that projected topographically to lateral tectum with responses that tended to habituate and those that lacked topography, responded weakly, and habituated rapidly. Axon tracing by localized retinal application of carbocyanine dyes supported the electrophysiological data. RGC soma counts were normal in both intact and axotomized RGC populations, contrasting with the 30% RGC loss after complete injury. Unlike incomplete optic nerve injury in mammals, where RGC axon regeneration fails and secondary cell death removes many intact RGC somata, lizards experience a “win–win” situation: intact RGC axons favorably influence the functional outcome for regenerating ones and RGCs do not succumb to either primary or secondary cell death. J. Comp. Neurol. 505:46–57, 2007. © 2007 Wiley‐Liss, Inc.
Metabolic and functional profiling of the normal rat retina
Authors: Sun Daniel , Vingrys Algis J. , Kalloniatis Michael 
Published: August 2007

AbstractWe established a metabolic and functional profile map of the normal rat retina, given the premise that: 1) amino acid neurochemistry reflects metabolic integrity and cellular identity, and 2) the permeation of a cation channel probe, agmatine (1‐amino‐4‐guanidobutane, AGB), reflects cation channel functionality. The purpose was to provide a unique method of simultaneously assessing the metabolic and functional characteristics of the normal retina, upon which a comparison can be made to disease models. Quantitative pattern recognition analysis of overlapping amino acid and AGB expression profiles was used to provide a statistically robust classification of all neural elements according to their metabolic and functional characteristics. This classification was spatially complete and with single‐cell resolution. The resulting classification demonstrated 28 statistically separable theme classes dominated by characteristic glutamate, GABA, glycine, and/or taurine profiles, with each of the neuronal theme classes containing further subtypes. The inclusion of a functional parameter (AGB mapping) in the classification process nearly doubled the number of neural elements that could be ascribed a neurochemical/cation profile, compared to when amino acid labeling was used alone. Strong endogenous glutamate gated AGB labeling was observed in horizontal cells, rod bipolar cells, cholinergic amacrine cells, and AII amacrine cells. The resulting amino acid and AGB profile matrix constitutes a nomogram for assessing cellular responses to experimental challenges in models of ocular disease. J. Comp. Neurol. 505:92–113, 2007. © 2007 Wiley‐Liss, Inc.
Metabolic and functional profiling of the ischemic/reperfused rat retina
Authors: Sun Daniel , Vingrys Algis J. , Kalloniatis Michael 
Published: August 2007

AbstractWe quantitatively tracked the recovery in amino acid labeling and cation channel functionality within distinct retinal elements for up to 2 weeks after an ischemic insult. Pattern recognition analysis of multiple amino acid and agmatine (a cation channel probe; 1‐amino‐4‐guanidobutane; AGB) immunocytochemical patterns was used to classify all neural elements within the retina. This classification was spatially complete and with single‐cell resolution. By 48 hours of reperfusion the amino acid labeling pattern of virtually all cell populations had returned to near preischemic levels, with the exception of glutamine and alanine levels, which remained significantly higher in many cell populations. Classification resulted in a total of 18 statistically separable theme classes (including neurons, glia, and extraretinal classes), a reduction of 10 theme classes from the normal retina (Sun et al. [2007a,b] J Comp Neurol, this issue). In addition to the known selective losses of amacrine cell types within the inner nuclear layer, we now demonstrate a selective loss of theme classes representing cone bipolar cells within the bipolar cell population. While there was a recovery in the amino acid labeling pattern, there were persistent cation channel gating anomalies (as reflected by AGB labeling) within several theme classes, including the theme class representing all the remaining rod bipolar cells, suggesting aberrant neuronal function secondary to metabolic insult. J. Comp. Neurol. 505:114–130, 2007. © 2007 Wiley‐Liss, Inc.
Translating immunological tolerance into therapy
Authors: Prakken Berent J. , Albani Salvatore , van Eden Willem 
Published: August 2007

AbstractThirty scientists from Japan, USA and Europe met from January 18th to 20th 2007 in a stormy Amsterdam for an expert meeting on translating immune tolerance into novel therapies. The meeting was held in the “Trippenhouse” a 16th century historical building, home of the Royal Netherlands Academy of Arts and Sciences, the host of the meeting.
Ceramide in Pseudomonas aeruginosa infections
Authors: Riethmüller Joachim , Riehle Andrea , Grassmé Heike , Gulbins Erich 
Published: August 2007

AbstractCystic fibrosis (CF), the most common autosomal recessive disorder, at least in western countries, is caused by mutations of the cystic fibrosis transmembranous conductance regulator (CFTR) molecule and affects approximately 80,000 patients in Europe and the USA. Most, if not all, CF patients develop a chronic pulmonary infection with Pseudomonas aeruginosa. At present it is unknown why CF patients are highly sensitive to P. aeruginosa infections, and most importantly, no curative treatment for CF is available. P. aeruginosa infection results in an activation of the enzyme acid sphingomyelinase which catalyzes the release of ceramide from sphingomyelin in the cell membrane. Ceramide forms large ceramide‐enriched membrane domains that are required for internalization of bacteria, induction of cell death in infected cells and a controlled release of cytokines from infected cells. Ceramide‐enriched membrane platforms seem to serve the reorganization of receptors and intracellular signaling molecules involved in the infection of mammalian cells with P. aeruginosa. The significance of the acid sphingomyelinase and ceramide for the infection of mammalian cells with P. aeruginosa was demonstrated on mice genetically deficient for the acid sphingomyelinase. Further studies with N. gonorrhoeae, S. aureus and rhinoviruses indicate that ceramide‐enriched membrane domains are also important for the infection of mammalian cells with other bacterial and viral pathogens, suggesting a general role of these membrane domains in infectious biology.
Lignan contents in sesame seeds and products
Authors: Moazzami Ali A. , Haese Stefanie L. , Kamal‐Eldin Afaf 
Published: August 2007

AbstractSesame seed (Sesamum indicum L.) is a rich source of furofuran lignans with a wide range of potential biological activities. The major lignans in sesame seeds are the oil‐soluble sesamin and sesamolin, as well as glucosides of sesaminol and sesamolinol that reside in the defatted sesame flour. Upon refining of sesame oil, acid‐catalyzed transformation of sesamin to episesamin and of sesamolin to epimeric sesaminols takes place, making the profile of refined sesame oils different from that of virgin oils. In this study, the total lignan content of 14 sesame seeds ranged between 405 and 1178 mg/100 g and the total lignan content in 14 different products, including tahini, ranged between 11 and 763 mg/100 g. The content of sesamin and sesamolin in ten commercial virgin and roasted sesame oils was in the range of 444–1601 mg/100 g oil. In five refined sesame oils, sesamin ranged between 118 and 401 mg/100 g seed, episesamin between 12 and 206 mg/100 g seed, and the total contents of sesaminol epimers between 5 and 35 mg/100 g seed, and no sesamolin was found. Thus, there is a great variation in the types and amounts of lignans in sesame seeds, seed products and oils. This knowledge is important for nutritionists working on resolving the connection between diet and health. Since the consumption of sesame seed products is increasing steadily in Europe and USA, it is important to include sesame seed lignans in databases and studies pertinent to the nutritional significance of antioxidants and phytoestrogens. It is also important to differentiate between virgin, roasted and refined sesame oils.
Coupling CE with atmospheric pressure photoionization MS for pharmaceutical basic compounds: Optimization of operating parameters
Authors: Schappler Julie , Guillarme Davy , Prat Josiane , Veuthey Jean‐Luc , Rudaz Serge 
Published: August 2007

AbstractThe use of CE coupled with MS (CE‐MS) has evolved as a useful tool to analyze charged species in small sample volumes. Because of its sensitivity, versatility and ease of implementation, the ESI interface is currently the method of choice to hyphenate CE to MS. An alternative can be the atmospheric pressure photoionization (APPI) source, however, numerous parameters must be optimized for its coupling to CE. After evaluation of the sheath liquid composition and the CE capillary outlet position, an experimental design methodology was assessed for optimizing other ionization source parameters, such as sheath liquid flow rate, drying gas flow rate and temperature, nebulizing gas pressure, vaporizer temperature, and capillary voltage. For this purpose, a fractional factorial design (FFD) was selected as a screening procedure to identify factors which significantly influence sensitivity and efficiency. A face‐centered central composite design (CCD) was then used to predict and optimize sensitivity, taking into account the most relevant variables. Sensitivity was finally evaluated with the optimized conditions and height‐to‐noise ratios (H/N) around 10 were achieved for an injection of 200 ng/mL of each analyte.
Multi‐phase evolution of gnammas (weathering pits) in a Holocene deglacial granite landscape, Minnesota (USA)
Authors: Domínguez‐Villar David , Jennings Carrie E. 
Published: August 2007

AbstractThe morphometry of 85 gnammas (weathering pits) from Big Stone County in western Minnesota allows the assessment of the relative ages of the gnamma population. The ratio between maximum and minimum depths is independent of the initial size of the cavity and only depends on the weathering evolution. Therefore, the distribution of depth ratios can be used to assess the gnamma population age and the history of weathering. The asymmetrical distribution of depth ratios measured in Big Stone County forms three distinct populations. When these sets are analyzed independently, the correlation (r2) between maximum and minimum depths is greater than 0·95. Each single population has a normal distribution of depth ratios and the average depth ratios (δ‐value) for each population are δ1 = 1·60 ± 0·05, δ2 = 2·09 ± 0·04 and δ3 = 2·42 ± 0·08.The initiation of gnamma formation followed the exhumation of the granite in the region. This granite was till and saprolite covered upon retreat of the ice from the Last Glacial Maximum. Nearby outcrops are striated, but the study site remained buried until it was exhumed by paleofloods issuing from a proglacial lake.These Holocene‐aged gnammas in western Minnesota were compared with gnammas of other ages from around the world. Our new results are in accordance with the hypothesis that δ‐values represent the evolution of gnammas with time under temperate‐ to cold‐climate dynamics. Phases of the formation of new gnammas may result from changes in weathering processes related to climate changes. Copyright © 2007 John Wiley & Sons, Ltd.
EWSR1‐CREB1 is the predominant gene fusion in angiomatoid fibrous histiocytoma
Authors: Antonescu Cristina R. , Dal Cin Paola , Nafa Khedoudja , Teot Lisa A. , Surti Urvashi , Fletcher Christopher D. , Ladanyi Marc 
Published: August 2007

AbstractThe molecular hallmark of angiomatoid fibrous histiocytoma (AFH) is not well defined, with only six cases with specific gene fusions reported to date, consisting of either FUS‐ATF1 or EWSR1‐ATF1. To address this, we investigated the presence of FUS‐ATF1, EWSR1‐ATF1, and the highly related EWSR1‐CREB1 fusion in a group of nine AFHs. All cases were subjected to RT‐PCR for EWSR1‐ATF1 and EWSR1‐CREB1. FISH for EWSR1 and FUS rearrangements was performed in most cases. Transcriptional profiling was performed in three tumors and their gene expression was compared to five clear cell sarcomas expressing either the EWSR1‐ATF1 or EWSR1‐CREB1 fusion. By RT‐PCR, eight out of nine tumors showed the presence of the EWSR1‐CREB1 fusion, while one had an EWSR1‐ATF1 transcript. FISH showed evidence of EWSR1 rearrangement in seven out of eight cases. Karyotypic analysis performed in one tumor showed a t(2;22)(q33;q12). High transcript levels were noted for TFE3 in AFH tumors, while overexpression of genes involved in melanogenesis, such as MITF, GP100, and MET was noted in somatic clear cell sarcomas. We report for the first time the presence of EWSR1‐CREB1 in AFH, which now appears to be the most frequent gene fusion in this tumor. EWSR1‐CREB1 is a novel translocation recently described in clear cell sarcoma of the GI tract. EWSR1‐ATF1, identified in some AFH cases, is the most common genetic abnormality in soft tissue clear cell sarcoma. Thus, identical fusions involving ATF1 and CREB1 are found in two distinct sarcomas, which may be able to transform two different types of mesenchymal precursor cells, unlike most other sarcoma gene fusions. © 2007 Wiley‐Liss, Inc.
Stratigraphic and geochronological context of human habitation along the Galana River, Kenya
Authors: Wright David K. , Forman Steven L. , Kusimba Chapurukha M. , Pierson James , Gomez Jeaneth , Tattersfield Peter 
Published: August 2007

AbstractGeoarchaeological investigations along the Galana River, eastern Kenya, document a pattern of channel aggradation and then degradation from the Middle to Late Holocene. Archaeological occupations at six sites in fluvial terraces along a ˜100 km stretch of the Galana River in Tsavo East National Park correspond with fluvial aggradation beginning ca. 6000 years ago. Artifact analyses indicate that the inhabitants of these sites utilized ceramics and stone tools similar to Pastoral Neolithic traditions detected at other penecontemporaneous archaeological sites in East Africa and possessed domesticated cattle from ca. 3700 years ago. The site occupations that occur during this period have dense artifact concentrations of predominantly locally procured items. The Galana River incised after ca. 900 years ago and there is a noticeable paucity of archaeological material, reflecting more peripatetic lifestyles. This shift in settlement pattern may reflect a decrease in reliance on riverine food sources during the Late Holocene, with diminished riparian environments associated with channel incision. © 2007 Wiley Periodicals, Inc.