bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endogenous bcl-2 is not required for the development of Eμ-myc–induced B-cell lymphoma
Authors: Kelly Priscilla N. , Puthalakath Hamsa , Adams Jerry M. , Strasser Andreas 
Published: February 2007

Abstract
Although myc and bcl-2 synergize in tumor development, particularly lymphomagenesis, it is not known whether endogenous bcl-2 is required for myc-induced tumorigenesis. To investigate the role of endogenous Bcl-2 in myc-induced lymphomagenesis, we bypassed the early death of Bcl-2–deficient mice by reconstituting lethally irradiated wild-type (wt) mice with a hematopoietic system from fetal liver–derived stem cells of Eμ-myc/bcl-2−/− or control Eμ-myc transgenic embryos. In premalignant (healthy) recipients, loss of Bcl-2 caused a moderate decrease in pre-B and immature B cells, and a dramatic reduction of mature B lymphocytes expressing the Eμ-myc transgene. Furthermore, cultured preneoplastic Eμ-myc/bcl-2−/− mature B cells displayed accelerated apoptosis compared with Eμ-myc B cells. However, despite the striking reduction in B-cell numbers in vivo, ablation of endogenous Bcl-2 did not prevent or even delay development of Eμ-myc lymphoma. Moribund mice presented with similar degrees of splenomegaly, blood leukocyte numbers, and tumor dissemination at death. These findings demonstrate that the initiation, development, continued growth, and severity of Eμ-myc lymphoma do not depend upon endogenous Bcl-2, nor upon the total number of B lymphoid cells driven by the Eμ-myc transgene. These results have implications for the treatment of hematopoietic tumors, particularly those that are not caused by Bcl-2 overexpression.
Considerations in the identification of functional RNA structural elements in genomic alignments
Authors: Babak Tomas , Blencowe Benjamin J , Hughes Timothy R 
Published: February 2007

Abstract

Background
Accurate identification of novel, functional noncoding (nc) RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries.

Results
We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component) was significantly higher for real than shuffled sequence, while the distribution for coding sequences was lower than that of corresponding shuffles.

Conclusion
Accurate prediction of novel RNA structural elements in genome sequence remains a difficult problem, and development of an appropriate negative-control strategy for multiple alignments is an important practical challenge. Nonetheless, the general trends we observed for the distributions of predicted ncRNAs across genomic features are biologically meaningful, supporting the presence of secondary structural elements in many 3' UTRs, and providing evidence for evolutionary selection against secondary structures in coding regions.
Conservation of the TRAPPII-specific subunits of a Ypt/Rab exchanger complex
Authors: Cox Randal , Chen Shu Hui , Yoo Eunice , Segev Nava 
Published: February 2007

AbstractBackgroundYpt/Rab GTPases and their GEF activators regulate intra-cellular trafficking in all eukaryotic cells. InS. cerivisiae, the modular TRAPP complex acts as a GEF for the Golgi gatekeepers: Ypt1 and the functional pair Ypt31/32. While TRAPPI, which acts in early Golgi, is conserved from fungi to animals, not much is known about TRAPPII, which acts in late Golgi and consists of TRAPPI plus three additional subunits.ResultsHere, we show a phylogenetic analysis of the three TRAPPII-specific subunits. One copy of each of the two essential subunits, Trs120 and Trs130, is present in almost every fully sequenced eukaryotic genome. Moreover, the primary, as well as the predicted secondary, structure of the Trs120- and Trs130-related sequences are conserved from fungi to animals. The mammalian orthologs of Trs120 and Trs130, NIBP and TMEM1, respectively, are candidates for human disorders. Currently, NIBP is implicated in signaling, and TMEM1 is suggested to have trans-membrane domains (TMDs) and to function as a membrane channel. However, we show here that the yeast Trs130 does not function as a trans-membrane protein, and the human TMEM1 does not contain putative TMDs. The non-essential subunit, Trs65, is conserved only among many fungi and some unicellular eukaryotes. Multiple alignment analysis of each TRAPPII-specific subunit revealed conserved domains that include highly conserved amino acids.ConclusionWe suggest that the function of both NIBP and TMEM1 in the regulation of intra-cellular trafficking is conserved from yeast to man. The conserved domains and amino acids discovered here can be used for functional analysis that should help to resolve the differences in the assigned functions of these proteins in fungi and animals.
Erratum to: Rapid chemokinetic movement and the invasive potential of lung cancer cells; a functional molecular study
Authors: Tchou-Wong Kam-Meng , Fok Sandra YY , Rubin Jeffrey S , Pixley Fiona , Condeelis John , Braet Filip , Rom William , Soon Lilian L 
Published: February 2007

Abstract
This is a correction of an earlier published article.
HNPCC versus sporadic microsatellite-unstable colon cancers follow different routes toward loss of HLA class I expression
Authors: Dierssen Jan Willem F , de Miranda Noel FCC , Ferrone Soldano , van Puijenbroek Marjo , Cornelisse Cees J , Fleuren Gert Jan , van Wezel Tom , Morreau Hans 
Published: February 2007

AbstractBackgroundAbnormalities in Human Leukocyte Antigen (HLA) class I expression are common in colorectal cancer. Since HLA expression is required to activate tumor antigen-specific cytotoxic T-lymphocytes (CTL), HLA class I abnormalities represent a mechanism by which tumors circumvent immune surveillance. Tumors with high microsatellite instability (MSI-H) are believed to face strong selective pressure to evade CTL activity since they produce large amounts of immunogenic peptides. Previous studies identified the prevalence of HLA class I alterations in MSI-H tumors. However, those reports did not compare the frequency of alterations between hereditary and sporadic MSI-H tumors neither the mechanisms that led to HLA class I alterations in each subgroup.MethodsTo characterize the HLA class I expression among sporadic MSI-H and microsatellite-stable (MSS) tumors, and HNPCC tumors we compared immunohistochemically the expression of HLA class I, β2-microglobulin (β2m), and Antigen Processing Machinery (APM) components in 81 right-sided sporadic and 75 HNPCC tumors. Moreover, we investigated the genetic basis for these changes.ResultsHLA class I loss was seen more frequently in MSI-H tumors than in MSS tumors (p < 0.0001). Distinct mechanisms were responsible for HLA class I loss in HNPCC and sporadic MSI-H tumors. Loss of HLA class I expression was associated with β2m loss in HNPCC tumors, but was correlated with APM component defects in sporadic MSI-H tumors (p < 0.0001). In about half of the cases, loss of expression of HLA class I was concordant with the detection of one or more mutations in theβ2mand APM components genes.ConclusionHLA class I aberrations are found at varying frequencies in different colorectal tumor types and are caused by distinct genetic mechanisms. Chiefly, sporadic and hereditary MSI-H tumors follow different routes toward HLA class I loss of expression supporting the idea that these tumors follow different evolutionary pathways in tumorigenesis. The resulting variation in immune escape mechanisms may have repercussions in tumor progression and behavior.
The federal government commissioner for patient issues in Germany: initial analysis of the user inquiries
Authors: Schneider Nils , Dierks Marie-Luise , Seidel Gabriele , Schwartz Friedrich W 
Published: February 2007

Abstract
Background
The political objective in many countries worldwide is to give better consideration to the interests of patients within the health system. The establishment of a federal government commissioner for the issues of patients in the health system in Germany in 2004 is part of these endeavours. The structure and field of activities of this institution has been unique so far. This study investigates for the first time the inquiries the commissioner receives from the public.

Methods
A 33% sampling (n = 850) of the written inquiries (correspondence and e-mails) addressed to the commissioner in the first six months of the year 2005 (n = 2580) was investigated. In a procedure comprising combined qualitative and quantitative levels, the material was thematically encoded and the inquiries allocated to the resulting categories (multiple nominations). The results are presented in descriptive form and investigated especially with respect to sex and age-specific differences. The interdependences between the categorized criteria are analysed.

Results
The inquirers are equally spread out amongst the sexes (49% women, 51% men). Older persons outweigh the younger (69% over 60 years). In most cases the issues take the form of claims (72%, n = 609). In every fifth inquiry (n = 168) the personal financial burden for health services is considered as being too high; about equally high (n = 159) is the proportion of persons who criticize the communication with health professionals, especially hospitals and doctors' surgeries. Every third who mentions a medical practice uses terms such as "uncertainty" and "anxiety". It is conspicuous that men more often than women write that they feel unfairly treated in the health system (62% vs. 38%, p < 0.05).

Conclusion
Predominantly older persons seek the assistance of the federal government commissioner for patient issues. Considerable uncertainty and anxiety with respect to services and charges within the system of the German health insurances become evident. It is not possible from the data to draw conclusions concerning the impact of the commissioner's work on the health system. Nor do we gain any knowledge about the usefulness of the service for the individual. Therefore, evaluation of the political impact and the user satisfaction should follow.
Preoperative external beam radiotherapy and reduced dose brachytherapy for carcinoma of the cervix: survival and pathological response
Authors: Jacinto Alexandre A , Castilho Marcus S , Novaes Paulo ERS , Novick Pablo R , Viani Gustavo A , Salvajoli João V , Ferrigno Robson , Pellizzon Antonio Cássio A , Lima Stella SS , Maia Maria AC , Fogaroli Ricardo C 
Published: February 2007

Abstract
Purpose
To evaluate the pathologic response of cervical carcinoma to external beam radiotherapy (EBRT) and high dose rate brachytherapy (HDRB) and outcome.

Materials and methods
Between 1992 and 2001, 67 patients with cervical carcinoma were submitted to preoperative radiotherapy. Sixty-five patients were stage IIb. Preoperative treatment included 45 Gy EBRT and 12 Gy HDRB. Patients were submitted to surgery after a mean time of 82 days. Lymphadenectomy was performed in 81% of patients. Eleven patients with residual cervix residual disease on pathological specimen were submitted to 2 additional insertions of HDRB.

Results
median follow up was 72 months. Five-year cause specific survival was 75%, overall survival 65%, local control 95%. Complete pelvic pathological response was seen in 40%. Surgery performed later than 80 days was associated with pathological response. Pelvic nodal involvement was found in 12%. Complete pelvic pathological response and negative lymphnodes were associated with better outcome (p = .03 and p = .005). Late grade 3 and 4 urinary and intestinal adverse effects were seen in 12 and 2% of patients.

Conclusion
Time allowed between RT and surgery correlated with pathological response. Pelvic pathological response was associated with improved outcome. Postoperative additional HDRB did not improve therapeutic results. Treatment was well tolerated.
Effects on osteoclast and osteoblast activities in cultured mouse calvarial bones by synovial fluids from patients with a loose joint prosthesis and from osteoarthritis patients
Authors: Andersson Martin K , Lundberg Pernilla , Ohlin Acke , Perry Mark J , Lie Anita , Stark André , Lerner Ulf H 
Published: February 2007

Abstract
Aseptic loosening of a joint prosthesis is associated with remodelling of bone tissue in the vicinity of the prosthesis. In the present study, we investigated the effects of synovial fluid (SF) from patients with a loose prosthetic component and periprosthetic osteolysis on osteoclast and osteoblast activities in vitro and made comparisons with the effects of SF from patients with osteoarthritis (OA). Bone resorption was assessed by the release of calcium 45 (45Ca) from cultured calvariae. The mRNA expression in calvarial bones of molecules known to be involved in osteoclast and osteoblast differentiation was assessed using semi-quantitative reverse transcription-polymerase chain reaction (PCR) and real-time PCR. SFs from patients with a loose joint prosthesis and patients with OA, but not SFs from healthy subjects, significantly enhanced 45Ca release, effects associated with increased mRNA expression of calcitonin receptor and tartrate-resistant acid phosphatase. The mRNA expression of receptor activator of nuclear factor-kappa-B ligand (rankl) and osteoprotegerin (opg) was enhanced by SFs from both patient categories. The mRNA expressions of nfat2 (nuclear factor of activated T cells 2) and oscar (osteoclast-associated receptor) were enhanced only by SFs from patients with OA, whereas the mRNA expressions of dap12 (DNAX-activating protein 12) and fcrγ (Fc receptor common gamma subunit) were not affected by either of the two SF types. Bone resorption induced by SFs was inhibited by addition of OPG. Antibodies neutralising interleukin (IL)-1α, IL-1β, soluble IL-6 receptor, IL-17, or tumour necrosis factor-α, when added to individual SFs, only occasionally decreased the bone-resorbing activity. The mRNA expression of alkaline phosphatase and osteocalcin was increased by SFs from patients with OA, whereas only osteocalcin mRNA was increased by SFs from patients with a loose prosthesis. Our findings demonstrate the presence of a factor (or factors) stimulating both osteoclast and osteoblast activities in SFs from patients with a loose joint prosthesis and periprosthetic osteolysis as well as in SFs from patients with OA. SF-induced bone resorption was dependent on activation of the RANKL/RANK/OPG pathway. The bone-resorbing activity could not be attributed solely to any of the known pro-inflammatory cytokines, well known to stimulate bone resorption, or to RANKL or prostaglandin E2 in SFs. The data indicate that SFs from patients with a loose prosthesis or with OA stimulate bone resorption and that SFs from patients with OA are more prone to enhance bone formation.
Esophageal Doppler-guided fluid management decreases blood lactate levels in multiple-trauma patients: a randomized controlled trial
Authors: Chytra Ivan , Pradl Richard , Bosman Roman , Pelnář Petr , Kasal Eduard , Židková Alexandra 
Published: February 2007

Abstract
Introduction
Esophageal Doppler was confirmed as a useful non-invasive tool for management of fluid replacement in elective surgery. The aim of this study was to assess the effect of early optimization of intravascular volume using esophageal Doppler on blood lactate levels and organ dysfunction development in comparison with standard hemodynamic management in multiple-trauma patients.

Methods
This was a randomized controlled trial. Multiple-trauma patients with blood loss of more than 2,000 ml admitted to the intensive care unit (ICU) were randomly assigned to the protocol group with esophageal Doppler monitoring and to the control group. Fluid resuscitation in the Doppler group was guided for the first 12 hours of ICU stay according to the protocol based on data obtained by esophageal Doppler, whereas control patients were managed conventionally. Blood lactate levels and organ dysfunction during ICU stay were evaluated.

Results
Eighty patients were randomly assigned to Doppler and 82 patients to control treatment. The Doppler group received more intravenous colloid during the first 12 hours of ICU stay (1,667 ± 426 ml versus 682 ± 322 ml; p < 0.0001), and blood lactate levels in the Doppler group were lower after 12 and 24 hours of treatment than in the control group (2.92 ± 0.54 mmol/l versus 3.23 ± 0.54 mmol/l [p = 0.0003] and 1.99 ± 0.44 mmol/l versus 2.37 ± 0.58 mmol/l [p < 0.0001], respectively). No difference in organ dysfunction between the groups was found. Fewer patients in the Doppler group developed infectious complications (15 [18.8%] versus 28 [34.1%]; relative risk = 0.5491; 95% confidence interval = 0.3180 to 0.9482; p = 0.032). ICU stay in the Doppler group was reduced from a median of 8.5 days (interquartile range [IQR] 6 to16) to 7 days (IQR 6 to 11) (p = 0.031), and hospital stay was decreased from a median of 17.5 days (IQR 11 to 29) to 14 days (IQR 8.25 to 21) (p = 0.045). No significant difference in ICU and hospital mortalities between the groups was found.

Conclusion
Optimization of intravascular volume using esophageal Doppler in multiple-trauma patients is associated with a decrease of blood lactate levels, a lower incidence of infectious complications, and a reduced duration of ICU and hospital stays.
Hyperoxia increases ventilator-induced lung injury via mitogen-activated protein kinases: a prospective, controlled animal experiment
Authors: Li Li-Fu , Liao Shuen-Kuei , Ko Yu-Shien , Lee Cheng-Huei , Quinn Deborah A 
Published: February 2007

Abstract
Introduction
Large-tidal volume (VT) mechanical ventilation and hyperoxia used in patients with acute respiratory distress syndrome can damage pulmonary epithelial cells through lung inflammation and apoptotic cell death. Hyperoxia has been shown to increase ventilator-induced lung injury, but the mechanisms regulating interaction between large VT and hyperoxia are unclear. We hypothesized that the addition of hyperoxia to large-VT ventilation would increase neutrophil infiltration by upregulation of the cytokine macrophage inflammatory protein-2 (MIP-2) and would increase apoptosis via the mitogen-activated protein kinase pathways.

Methods
C57BL/6 mice were exposed to high-VT (30 ml/kg) mechanical ventilation with room air or hyperoxia for one to five hours.

Results
The addition of hyperoxia to high-VT ventilation augmented lung injury, as demonstrated by increased apoptotic cell death, neutrophil migration into the lung, MIP-2 production, MIP-2 mRNA expression, increased DNA binding activity of activator protein-1, increased microvascular permeability, and c-Jun NH2-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) 1/2 activation. Hyperoxia-induced augmentation of high-VT-induced lung injury was attenuated in JNK-deficient mice and in mice with pharmacologic inhibition of ERK activity by PD98059. However, only JNK-deficient mice, and not mice with ERK activity inhibition by PD98059, were protected from high-VT-induced lung injury without hyperoxia.

Conclusion
We conclude that hyperoxia increased high-VT-induced cytokine production, neutrophil influx, and apoptotic cell death through activation of the JNK and ERK1/2 pathways.
One-Step Rapid Reverse Transcription–PCR Assay for Detecting and Typing Dengue Viruses with GC Tail and Induced Fluorescence Resonance Energy Transfer Techniques for Melting Temperature and Color Multiplexing
Authors: Lo Constance LH , Yip Shea Ping , Cheng Peter KC , To Tony SS , Lim Wilina WL , Leung Polly HM 
Published: February 2007

Abstract
Background: Dengue fever is an arthropod-borne infection caused by dengue viruses (DVs; DEN-1 to DEN-4). Early diagnosis is critical to prevent severe disease progression and the spreading of DV because no vaccine or specific treatment is available; therefore, a rapid and specific diagnostic assay capable of detecting and typing all serotypes would be ideal.
Methods: We amplified RNA samples from all 4 DV serotypes and Japanese encephalitis virus with 4 serotype-specific forward primers and a universal species-specific reverse primer. DEN-1 and DEN-3 forward primers were labeled at their 5′ ends with BODIPY 630/650 and Cy5.5, respectively. DEN-1 and DEN-3 amplicons were detected by their characteristic emission generated from induced fluorescence resonance energy transfer. The presence of DEN-2 and DEN-4 amplicons was indicated by SYBR Green I (SGI) signals at specific amplicon melting temperatures (Tms).
Results: Fluorescence signals with specific emission wavelengths were obtained from DEN-1 and DEN-3. SGI melting profiles showed a Tm difference between DEN-2 and DEN-4 of 4.7 °C, which was sufficient for differentiating these 2 serotypes. The primers did not amplify the Japanese encephalitis virus. The detection limits of DEN-1 to DEN-4 were 1.64 × 10−4, 1.05 × 10−3, 8.15 × 10−4, and 5.80 × 10−3 plaque-forming units per reaction, respectively. The assay had a dynamic range of 103–108 plaque-forming units/L and could be performed in 2 h.
Conclusions: A single-tube, 1-step reverse transcription–PCR assay based on Tm and color multiplexing was developed for detecting and typing all 4 DV serotypes.
Die Konzilien des byzantinischen Bilderstreits
Authors: Thümmel Hans Georg 
Published: February 2007

Abstract
The article is a sort of summary of more extensive studies published in “Die Konzilien zur Bilderfrage im 8. und 9. Jahrhundert, 2005”. The problems are reduced to three points: 1. In Byzantium during the eighth/ninth century the emperor was the only person responsible for theology and church politics. Thus, the councils duty was not to discuss problems, but to confirm the emperor's decision. 2. At the Seventh Ecumenical Council Tarasios used the idea of “pentarchy” as his main argument. But at the latest with the Arabic expansion of the seventh century three of the five patriarchies were no longer part of the “Reichskirche” and in the eighth century Rome took its bearing to the Francs. The concept to understand the unity of the church as the unity of the five patriarchs was used when the real basis for it was actually no longer given. 3. In the sixth century the picture in the Eastern Church gained in importance. It is an object, that works miracles and therefore receives veneration. Emperors who considered this to be superstitious forbade pictures (icons). A third position acknowledged pictures for didactical reasons and commemoration. This legitimated pictures on councils, while once admitted, customs considered superstitious were again introduced in Eastern Church.