bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inheritance of photoperiod‐sensitivity genes controlling flower initiation in sorghum, Sorghum bicolor Moench
Authors: Tarumoto Isao , Yanase Masanori , Kadowaki Hiroki , Yamada Tohru , Kasuga Shigemitu 
Published: April 2005

AbstractThe existence of a sorghum (Sorghum bicolor Moench) photoperiod sensitivity gene has been proposed to account for postponing flower initiation until Tentaka and Kazetachi meet with short daylengths below 12.5 h. To investigate the inheritance of this gene, three parental varieties, F1, F2, BC1F1 and BC1F2 populations of Tentaka and Kazetachi were evaluated for days‐to‐emergence of flag leaf (DEFL) under the field condition of long daylength (>13 h) and minimum temperatures over 20°C for at least 51 days after sowing in 1999, 2000 and 2001. The F1 hybrids, Tentaka (MS79 × Chohin232) and Kazetachi (MS138 × Chohin232), showed strong photoperiod sensitivity and very late DEFL, in spite of the photoperiod insensitivity of their parental varieties. In two different F2 populations, the segregation of early, middle and late plants for DEFL fitted in with the expected ratio of 7 : 30 : 27 under the three genes hypothesis, TtD1d1D2d2 for Tentaka and Kazetachi. Additionally, the expected ratio of early : middle : late (1 : 2 : 1) was observed in the segregation of BC1F1 of Tentaka × Chohin232 and Kazetachi × Chohin232 in 2000. These results suggest that two photoperiod sensitivity genes, D1 and D2 which show complementary dominant effects, are existent and the flowering phenotype of Tentaka and Kazetachi are expressed by the interactive operation both of a dominant thermo‐sensitivity gene (T) and complementary dominant photoperiod sensitivity genes (D1, D2), that is, the genotype TtD1d1D2d2.
Torture: Flesh, Truth, and the Fourth Gospel
Authors: Glancy Jennifer 
Published: April 2005

AbstractIn the Roman world, torture, conceived as a mechanism to extract truth from flesh, was used in judicial interrogation, most commonly in interrogation of slaves and other low-status persons. The flogging of Jesus in John 19:1-3, a flogging that occurs in the midst of the trial before Pilate, is best read as an instance of such judicial torture. If understood as an act of judicial torture, the flogging is also an act of witnessing to the truth: the flesh of the Johannine Jesus is flush with truth (John 1:14). And because Jesus' flesh is flush with truth, the Johannine passion narrative is an account of torture, torture as defined in Roman law: "By torture we mean the infliction of anguish and agony on the body to elicit the truth" (Dig. 48.10.15.41). As I trace the lineaments of truth in Jesus' corpus, I ask how the Fourth Gospel implicates the project of torture. Confronted by the horror of a U.S. policy of distilling truth from foreign bodies, I ask this question urgently. Is it possible to embrace flesh as a locus of truth and still to condemn the practice of torture? Through my carnal reading of the Johannine passion narrative, I attempt to do so.
Altered expression of membrane-bound and soluble CD95/Fas contributes to the resistance of fibrotic lung fibroblasts to FasL induced apoptosis
Authors: Bühling Frank , Wille Aline , Röcken Christoph , Wiesner Olaf , Baier Anja , Meinecke Ingmar , Welte Tobias , Pap Thomas 
Published: April 2005

Abstract
Background
An altered susceptibility of lung fibroblasts to Fas-induced apoptosis has been implicated in the pathogenesis of pulmonary fibrosis; however, the underlying mechanism is not completely understood. Here, we studied the susceptibility of lung fibroblasts, obtained from patients with (f-fibs) and without pulmonary fibrosis (n-fibs), to FasL- (CD95L/APO-1) induced apoptosis in relation to the expression and the amounts of membrane-bound and soluble Fas. We also analysed the effects of tumor necrosis factor-β on FasL-induced cell death.

Methods
Apoptosis was induced with recombinant human FasL, with and without prior stimulation of the fibroblasts with tumor necrosis factor-α and measured by a histone fragmentation assay and flow cytometry. The expression of Fas mRNA was determined by quantitative PCR. The expression of cell surface Fas was determined by flow cytometry, and that of soluble Fas (sFas) was determined by enzyme-linked immunosorbent assay.

Results
When compared to n-fibs, f-fibs were resistant to FasL-induced apoptosis, despite significantly higher levels of Fas mRNA. F-fibs showed lower expression of surface-bound Fas but higher levels of sFas. While TNF-α increased the susceptibility to FasL-induced apoptosis in n-fibs, it had no pro-apoptotic effect in f-fibs.

Conclusions
The data suggest that lower expression of surface Fas, but higher levels of apoptosis-inhibiting sFas, contribute to the resistance of fibroblasts in lung fibrosis against apoptosis, to increased cellularity and also to increased formation and deposition of extracellular matrix.
Evolutionary distance estimation and fidelity of pair wise sequence alignment
Authors: Rosenberg Michael S 
Published: April 2005

Abstract
Background
Evolutionary distances are a critical measure in comparative genomics and molecular evolutionary biology. A simulation study was used to examine the effect of alignment accuracy of DNA sequences on evolutionary distance estimation.

Results
Under the studied conditions, distance estimation was relatively unaffected by alignment error (50% or more of the sites incorrectly aligned) as long as 50% or more of the sites were identical among the sequences (observed P-distance < 0.5). Beyond this threshold, the alignment procedure artificially inflates the apparent sequence identity, skewing distance estimates, and creating alignments that are essentially indistinguishable from random data. This general result was independent of substitution model, sequence length, and insertion and deletion size and rate.

Conclusion
Examination of the estimated sequence identity may yield some guidance as to the accuracy of the alignment. Inaccurate alignments are expected to have large effects on analyses dependent on site specificity, but analyses that depend on evolutionary distance may be somewhat robust to alignment error as long as fewer than half of the sites have diverged.
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss)
Authors: Rexroad Caird E , Rodriguez Maria F , Coulibaly Issa , Gharbi Karim , Danzmann Roy G , DeKoning Jenefer , Phillips Ruth , Palti Yniv 
Published: April 2005

Abstract
Background
Comparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced.

Results
Eighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes.

Conclusion
The addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species.
Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors
Authors: Stull Robert A , Tavassoli Roya , Kennedy Scot , Osborn Steve , Harte Rachel , Lu Yan , Napier Cheryl , Abo Arie , Chin Daniel J 
Published: April 2005

Abstract
Background
Since the early stages of tumorigenesis involve adhesion, escape from immune surveillance, vascularization and angiogenesis, we devised a strategy to study the expression profiles of all publicly known and putative secreted and cell surface genes. We designed a custom oligonucleotide microarray containing probes for 3531 secreted and cell surface genes to study 5 diverse human transformed cell lines and their derivative xenograft tumors. The origins of these human cell lines were lung (A549), breast (MDA MB-231), colon (HCT-116), ovarian (SK-OV-3) and prostate (PC3) carcinomas.

Results
Three different analyses were performed: (1) A PCA-based linear discriminant analysis identified a 54 gene profile characteristic of all tumors, (2) Application of MANOVA (Pcorr < .05) to tumor data revealed a larger set of 149 differentially expressed genes. (3) After MANOVA was performed on data from individual tumors, a comparison of differential genes amongst all tumor types revealed 12 common differential genes. Seven of the 12 genes were identified by all three analytical methods. These included late angiogenic, morphogenic and extracellular matrix genes such as ANGPTL4, COL1A1, GP2, GPR57, LAMB3, PCDHB9 and PTGER3. The differential expression of ANGPTL4 and COL1A1 and other genes was confirmed by quantitative PCR.

Conclusion
Overall, a comparison of the three analyses revealed an expression pattern indicative of late angiogenic processes. These results show that a xenograft model using multiple cell lines of diverse tissue origin can identify common tumorigenic cell surface or secreted molecules that may be important biomarker and therapeutic discoveries.
Accumulation of marginal zone B cells and accelerated loss of follicular dendritic cells in NF-κB p50-deficient mice
Authors: Ferguson Andrew R , Corley Ronald B 
Published: April 2005

Abstract
Background
Marginal zone (MZ) B cells play important roles in the early phases of humoral immune responses. In addition to possessing an inherent capacity to rapidly differentiate into antibody secreting cells, MZ B cells also help to regulate the fate of both T-independent and T-dependent blood-borne antigens in the spleen. For T-dependent antigens, MZ B cells bind IgM-antigen complexes in a complement-dependent manner. Once MZ B cells bind IgM-containing immune complexes (IgM-IC), they transport them into B cell follicles for deposition onto follicular dendritic cells (FDCs), an important component of secreted IgM's ability to enhance adaptive immune responses. To further define the requirement for MZ B cells in IgM-IC deposition, mice deficient in the NF-κB protein p50, which have been reported to lack MZ B cells, were analyzed for their ability to trap IgM-IC onto FDCs.

Results
Mice (2 months of age) deficient in p50 (p50-/-) had small numbers of MZ B cells, as determined by cell surface phenotype and localization in the splenic MZ. These cells bound high levels of IgM-IC both in vivo and in vitro. Subsequent to the binding of IgM-IC by the MZ B cells in p50-/- mice, small amounts of IgM-IC were found localized on FDCs, suggesting that the MZ B cells retained their ability to transport these complexes into splenic follicles. Strikingly, MZ B cells accumulated with age in p50-/- mice. By 6 months of age, p50-/- mice contained normal numbers of these cells as defined by CD21/CD23 profile and high level expression of CD1d, CD9, and IgM, and by their positioning around the marginal sinus. However, FDCs from these older p50-/- mice exhibited a reduced capacity to trap IgM-IC and retain complement components.

Conclusion
These results demonstrate that while the p50 component of the NF-κB transcription complex plays an important role in the early development of MZ B cells, MZ B cells can develop and accumulate in mice lacking this protein. These results highlight the interface between genetic deficiencies and age, and suggest that different transcription factors may play distinct roles in the development and maintenance of cell populations at different ages.
Expression of a novel carbonic anhydrase, CA XIII, in normal and neoplastic colorectal mucosa
Authors: Kummola Laura , Hämäläinen Jonna M , Kivelä Jyrki , Kivelä Antti J , Saarnio Juha , Karttunen Tuomo , Parkkila Seppo 
Published: April 2005

Abstract
Background
Carbonic anhydrase (CA) isozymes may have an important role in cancer development. Some isozymes control pH homeostasis in tumors that appears to modulate the behaviour of cancer cells. CA XIII is the newest member of the CA gene family. It is a cytosolic isozyme which is expressed in a number of normal tissues. The present study was designed to investigate CA XIII expression in prospectively collected colorectal tumor samples.

Methods
Both neoplastic and normal tissue specimens were obtained from the same patients. The analyses were performed using CA XIII-specific antibodies and an immunohistochemical staining method. For comparison, the tissue sections were immunostained for other cytosolic isozymes, CA I and II.

Results
The results indicated that the expression of CA XIII is down-regulated in tumor cells compared to the normal tissue. The lowest signal was detected in carcinoma samples. This pattern of expression was quite parallel for CA I and II.

Conclusion
The down-regulation of cytosolic CA I, II and XIII in colorectal cancer may result from reduced levels of a common transcription factor or loss of closely linked CA1, CA2 and CA13 alleles on chromosome 8. Their possible role as tumor suppressors should be further evaluated.
Changes in characteristics of veterans using the VHA health care system between 1996 and 1999
Authors: Liu Chuan-Fen , Maciejewski Matthew L , Sales Anne EB 
Published: April 2005

Abstract
Background
The Department of Veterans Affairs' Veterans Health Administration (VHA) provides a health care safety net to veterans. This study examined changes in characteristics of veterans using the VHA health care system between 1996 and 1999 when VHA implemented major organizational changes to improve access of ambulatory care and to provide care to more veterans.

Methods
The study used two cross-sectional samples of the Medical Expenditures Panel Survey (MEPS), a national representative survey, in 1996 and 1999. The 1996 MEPS survey included 1,944 veterans and the 1999 MEPS survey included 1,974 veterans. There were 534 veterans and 740 veterans who used VHA services in 1996 and 1999, respectively.

Results
The proportion of veterans using the VHA system increased from 12.4% in 1996 to 14.6% in 1999. In both years, veterans were more likely to use VHA care if they were older, male, less educated, uninsured, unemployed, and in fair or poor health status. Only two variables, marital status and income, were different between the two years. Married veterans were more likely to use VHA care in 1999, but not in 1996. Veterans with higher incomes had greater odds of using VHA care in 1996, but there was no significant association between income and VHA use in 1999.

Conclusion
Characteristics of VHA users did not fundamentally change despite the reorganization of VHA health care delivery system and changes in eligibility and enrollment policy. The VHA system maintains its safety net mission while attracting more veterans.
Recognizing scientific excellence in the biology of cell adhesion
Authors: Wary Kishore K 
Published: April 2005

Abstract
The prestigious 2005 Japan Prize for Cell Biology has been awarded to Dr. Masatoshi Takeichi, Director of RIKEN Developmental Biology, Kobe, Japan, and Dr. Erkki Ruoslahti, Distinguished Professor, The Burnham Institute, La Jolla, USA for their "Fundamental contribution in elucidating the molecular mechanisms of cell adhesion". The award is scheduled to be presented to the scientists in ceremonies in Tokyo on April 20, 2005 as part of a week-long celebration of "Japan Prize Week".
Response Assessment of Aggressive Non-Hodgkin’s Lymphoma by Integrated International Workshop Criteria and Fluorine-18–Fluorodeoxyglucose Positron Emission Tomography
Authors: Juweid Malik E. , Wiseman Gregory A. , Vose Julie M. , Ritchie Justine M. , Menda Yusuf , Wooldridge James E. , Mottaghy Felix M. , Rohren Eric M. , Blumstein Norbert M. , Stolpen Alan , Link Brian K. , Reske Sven N. , Graham Michael M. , Cheson Bruce D. 
Published: April 2005

Purpose To determine whether a response classification based on integration of fluorine-18–fluorodeoxyglucose positron emission tomography (FDG-PET) into the International Workshop Criteria (IWC) provides a more accurate response assessment than IWC alone in patients with non-Hodgkin's lymphoma (NHL). Patients and Methods Fifty-four patients with aggressive NHL who underwent FDG-PET and computed tomography 1 to 16 weeks after four to eight cycles of chemotherapy with cyclophosphamide, doxorubicin, vincristine, and prednisone were assessed for complete response (CR), unconfirmed CR (CRu), partial response (PR), stable disease (SD), and progressive disease (PD) by the IWC and by integrated IWC and FDG-PET (IWC+PET). Progression-free survival (PFS) was also compared between IWC- and IWC+PET-assigned response designations. Results By IWC, 17 patients had a CR, seven had a CRu, 19 had a PR, nine had SD, and two had PD. In comparison, by IWC+PET, 35 patients had a CR, 12 had a PR, six had SD, one had PD, and zero had a CRu. In separate multivariate models, PFS was significantly shorter in patients with PR than in those with a CR using IWC (hazard ratio [HR], 8.9; P = .021) or IWC+PET (HR, 29.7; P = .0003). However, when the two classifications were included in the same multivariate model, only IWC+PET was a statistically significant independent predictor for PFS (P = .008 v P = .72 for IWC). In addition, when patients with a PR by IWC and a CR by IWC+PET were compared with those with a CR by IWC and a CR by IWC+PET, there was no significant difference in PFS (HR, 1.6; P = .72), indicating that IWC+PET identified a subset of IWC-PR patients with a more favorable prognosis. Conclusion Compared with IWC, the IWC+PET-based assessment provides a more accurate response classification in patients with aggressive NHL.
Randomized Comparison of ABVD Chemotherapy With a Strategy That Includes Radiation Therapy in Patients With Limited-Stage Hodgkin’s Lymphoma: National Cancer Institute of Canada Clinical Trials Group and the Eastern Cooperative Oncology Group
Authors: Meyer Ralph M. , Gospodarowicz Mary K. , Connors Joseph M. , Pearcey Robert G. , Bezjak Andrea , Wells Woodrow A. , Burns Bruce F. , Winter Jane N. , Horning Sandra J. , Dar A. Rashid , Djurfeldt Marina S. , Ding Keyue , Shepherd Lois E. 
Published: April 2005

Purpose We report results of a randomized trial comparing ABVD (doxorubicin, bleomycin, vinblastine, and dacarbazine) chemotherapy alone with treatment that includes radiation therapy in patients with limited-stage Hodgkin's lymphoma. Patients and Methods Patients with nonbulky clinical stage I to IIA Hodgkin's lymphoma were stratified into favorable and unfavorable risk cohorts. Patients allocated to radiation-containing therapy received subtotal nodal radiation if favorable risk or combined-modality therapy if unfavorable risk. Patients allocated to ABVD received four to six treatment cycles. Results We evaluated 399 patients. Median follow-up is 4.2 years. In comparison with ABVD alone, 5-year freedom from disease progression is superior in patients allocated to radiation therapy (P = .006; 93% v 87%); no differences in event-free survival (P = .06; 88% v 86%) or overall survival (P = .4; 94% v 96%) were detected. In a subset analyses comparing patients stratified into the unfavorable cohort, freedom from disease progression was superior in patients allocated to combined-modality treatment (P = .004; 95% v 88%); no difference in overall survival was detected (P = .3; 92% v 95%). Of 15 deaths observed, nine were attributed to causes other than Hodgkin's lymphoma or acute treatment-related toxicity. Conclusion In patients with limited-stage Hodgkin's lymphoma, no difference in overall survival was detected between patients randomly assigned to receive treatment that includes radiation therapy or ABVD alone. Although 5-year freedom from disease progression was superior in patients receiving radiation therapy, this advantage is offset by deaths due to causes other than progressive Hodgkin's lymphoma or acute treatment-related toxicity.
Phase III Study of the Eastern Cooperative Oncology Group (ECOG 2597): Induction Chemotherapy Followed by Either Standard Thoracic Radiotherapy or Hyperfractionated Accelerated Radiotherapy for Patients With Unresectable Stage IIIA and B Non–Small-Cell Lung Cancer
Authors: Belani Chandra P. , Wang Wei , Johnson David H. , Wagner Henry , Schiller Joan , Veeder Michael , Mehta Minesh 
Published: April 2005

Purpose To compare once-daily radiation therapy (qdRT) with hyperfractionated accelerated radiation therapy (HART) after two cycles of induction chemotherapy. Patients and Methods Eligible patients were treatment naive, and had stage IIIA and B unresectable non-small-cell lung cancer, Eastern Cooperative Oncology Group performance status 0/1, and normal organ function. Induction chemotherapy consisted of two cycles of carboplatin area under time-concentration curve 6 mg/mL · min plus paclitaxel 225 mg/m2 on day 1. RT consisted of arm 1 (qdRT), 64 Gy (2 Gy/d), versus arm 2 (HART), 57.6 Gy (1.5 Gy tid for 2.5 weeks). A total of 388 patients were needed to detect a 50% increase in median survival from 14 months of qdRT to 21 months of HART; accrual was not achieved and the study closed prematurely. Results Of 141 patients enrolled, 83% were randomly assigned after chemotherapy to qdRT (n = 59) or HART (n = 60). Median survival was 20.3 and 14.9 months for HART and qdRT, respectively (P = .28). Overall response was 25% and 22% for HART and qdRT, respectively (P = .69). Two- and 3-year survival was 44% and 34% for HART, and 24% and 14% for qdRT, respectively. Grade ≥ 3 toxicities included esophagitis in 14 v nine patients, and pneumonitis in 0 v 6 patients for HART and qdRT, respectively. Any subsequent trials of the HART regimen must address the issues that led to early closure, including slow accrual, logistics of HART, mucosal toxicity, and the fact that concurrent chemoradiotherapy now seems more effective than sequential treatment. Conclusion After two cycles of induction chemotherapy with carboplatin-paclitaxel, HART is feasible with an acceptable toxicity profile. Although statistical significance was not achieved and the study closed early, there was a positive statistical trend suggesting a survival advantage with the HART regimen.