bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis of Tropheryma whipplei strains reveals that diversity among clinical isolates is mainly related to the WiSP proteins
Authors: La My-Van , Crapoulet Nicolas , Barbry Pascal , Raoult Didier , Renesto Patricia 
Published: October 2007

AbstractBackgroundThe aim of this study was to analyze the genomic diversity of severalTropheryma whippleistrains by microarray-based comparative genomic hybridization. Fifteen clinical isolates originating from biopsy samples recovered from different countries were compared with theT. whippleiTwist strain. For each isolate, the genes were defined as either present or absent/divergent using the GACK analysis software. Genomic changes were then further characterized by PCR and sequencing.ResultsThe results revealed a limited genetic variation among theT. whippleiisolates, with at most 2.24% of the probes exhibiting differential hybridization against the Twist strain. The main variation was found in genes encoding the WiSP membrane protein family. This work also demonstrated a 19.2 kb-pair deletion within theT. whippleiDIG15 strain. This deletion occurs in the same region as the previously described large genomic rearrangement between Twist and TW08/27. Thus, this can be considered as a major hot-spot for intra-specificT. whippleidifferentiation. Analysis of this deleted region confirmed the role of WND domains in generatingT. whippleidiversity.ConclusionThis work provides the first comprehensive genomic comparison of severalT. whippleiisolates. It reveals that clinical isolates originating from various geographic and biological sources exhibit a high conservation rate, indicating thatT. whippleirarely interacts with exogenous DNA. Remarkably, frequent inter-strain variations were dicovered that affected members of the WiSP family.
RETRACTED ARTICLE: Agmatine protects retinal ganglion cells from hypoxia-induced apoptosis in transformed rat retinal ganglion cell line
Authors: Hong Samin , Lee Jong Eun , Kim Chan Yun , Seong Gong Je 
Published: October 2007

AbstractBackgroundAgmatine is an endogenous polyamine formed by the decarboxylation of L-arginine. We investigated the protective effects of agmatine against hypoxia-induced apoptosis of immortalized rat retinal ganglion cells (RGC-5). RGC-5 cells were cultured in a closed hypoxic chamber (5% O2) with or without agmatine. Cell viability was determined by lactate dehydrogenase (LDH) assay and apoptosis was examined by annexin V and caspase-3 assays. Expression and phosphorylation of mitogen-activated protein kinases (MAPKs; JNK, ERK p44/42, and p38) and nuclear factor-kappa B (NF-κB) were investigated by Western immunoblot analysis. The effects of agmatine were compared to those of brain-derived neurotrophic factor (BDNF), a well-known protective neurotrophin for retinal ganglion cells.ResultsAfter 48 hours of hypoxic culture, the LDH assay showed 52.3% cell loss, which was reduced to 25.6% and 30.1% when agmatine and BDNF were administered, respectively. This observed cell loss was due to apoptotic cell death, as established by annexin V and caspase-3 assays. Although total expression of MAPKs and NF-κB was not influenced by hypoxic injury, phosphorylation of these two proteins was increased. Agmatine reduced phosphorylation of JNK and NF-κB, while BDNF suppressed phosphorylation of ERK and p38.ConclusionOur results show that agmatine has neuroprotective effects against hypoxia-induced retinal ganglion cell damage in RGC-5 cells and that its effects may act through the JNK and NF-κB signaling pathways. Our data suggest that agmatine may lead to a novel therapeutic strategy to reduce retinal ganglion cell injury related to hypoxia.
X-ray structures of two proteins belonging to Pfam DUF178 revealed unexpected structural similarity to the DUF191 Pfam family
Authors: Tyagi Rajiv , Burley Stephen K , Swaminathan Subramanyam 
Published: October 2007

Abstract

Background
Pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. Pfam has two large series of functionally uncharacterized families, known as Domains of Unknown Function (DUFs) and Uncharacterized Protein Families (UPFs).

Results
Crystal structures of two proteins from Deinococcus radiodurans and Streptomyces coelicolor belonging to Pfam protein family DUF178 (ID: PF02621) have been determined using Selenium-Single-wavelength Anomalous Dispersion (Se-SAD). Based on the structure, we have identified the putative function for this family of protein.

Conclusion
Unexpectedly, we found that DUF178 Pfam is remarkably similar to Pfam family DUF191 suggesting that the sequence-based classification alone may not be sufficient to classify proteins into Pfam families.
Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides
Authors: Scotter Andrew J , Guo Meng , Tomczak Melanie M , Daley Margaret E , Campbell Robert L , Oko Richard J , Bateman David A , Chakrabartty Avijit , Sykes Brian D , Davies Peter L 
Published: October 2007

Abstract

Background
A right-handed, calcium-dependent β-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide.

Results
Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments.

Conclusion
Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties.
Patterns of tumor response in canine and feline cancer patients treated with electrochemotherapy: preclinical data for the standardization of this treatment in pets and humans
Authors: Spugnini Enrico P , Baldi Feliciano , Mellone Pasquale , Feroce Florinda , D'Avino Alfredo , Bonetto Francesco , Vincenzi Bruno , Citro Gennaro , Baldi Alfonso 
Published: October 2007

AbstractElectrochemotherapy (ECT) is a novel anticancer therapy that is currently being evaluated in human and pet cancer patients. ECT associates the administration of an anti-tumor agent to the delivery of trains of appropriate waveforms. The increased uptake of chemotherapy leads to apoptotic death of the neoplasm thus resulting in prolonged local control and extended survival. In this paper we describe the histological features of a broad array of spontaneous tumors of companion animals receiving pulse-mediated chemotherapy. Multivariate statistical analysis of the percentage of necrosis and apoptosis in the tumors before and after ECT treatment, shows that only a high percentage of necrosis and apoptosis after the ECT treatment were significantly correlated with longer survivals of the patients (p < 0.0001 and p = 0.004, respectively). Further studies on this topic are warranted in companion animals with spontaneous tumors to identify new molecular targets for electrochemotherapy and to the develop new therapeutical protocols to be translated to humans.
Dopaminergic regeneration by neurturin-overexpressing c17.2 neural stem cells in a rat model of Parkinson's disease
Authors: Liu Wei-Guo , Wang Xi-Jing , Lu Guo-Qiang , Li Biao , Wang Gang , Chen Sheng-Di 
Published: October 2007

AbstractBackgroundGenetically engineered neural stem cell (NSC) lines are promising vectors for the treatment of neurodegenerative diseases, particularly Parkinson's disease (PD). Neurturin (NTN), a member of the glial cell line-derived neurotrophic factor (GDNF) family, has been demonstrated to act specifically on mesencephalic dopaminergic neurons, suggesting its therapeutic potential for PD. In our previous work, we demonstrated that NTN-overexpressing c17.2 NSCs exerted dopaminergic neuroprotection in a rat model of PD. In this study, we transplanted NTN-c17.2 into the striatum of the 6-hydroxydopamine (6-OHDA) PD model to further determine the regenerative effect of NTN-c17.2 on the rat models of PD.ResultsAfter intrastriatal grafting, NTN-c17.2 cells differentiated and gradually downregulated nestin expression, while the grafts stably overexpressed NTN. Further, an observation of rotational behavior and the contents of neurotransmitters tested by high-performance liquid chromatography showed that the regenerative effect of the NTN-c17.2 group was significantly better than that of the Mock-c17.2 group, and the regenerative effect of the Mock-c17.2 group was better than that of the PBS group. Further research through reverse-transcriptase polymerase chain reaction assays and in vivo histology revealed that the regenerative effect of Mock-c17.2 and NTN-c17.2 cell grafts may be attributed to the ability of NSCs to produce neurotrophic factors and differentiate into tyrosine hydroxylase-positive cells.ConclusionThe transplantation of NTN-c17.2 can exert neuroregenerative effects in the rat model of PD, and the delivery of NTN by NSCs may constitute a very useful strategy in the treatment of PD.
Comparison of different commercial kits for HER2 testing in breast cancer: looking for the accurate cutoff for amplification
Authors: Cayre Anne , Mishellany Florence , Lagarde Nicole , Penault-Llorca Frédérique 
Published: October 2007

Abstract
Introduction
Accurate determination of human epidermal growth factor receptor 2 (HER2) status is essential for optimal patient management with trastuzumab (Herceptin). However, standard guidelines do not specify a particular commercial kit, antibody or probe for testing, and discrepancies arise from variability between kits. The aim of this study was to compare the accuracy of four commercially available fluorescence/chromogenic in situ hybridisation (FISH/CISH) kits and validate one for the resolution of borderline immunohistochemistry (IHC) cases. The interpretation pitfalls, optimal threshold values, assay duration and complexity of each kit were also considered.

Methods
The Food and Drug Administration (FDA)-approved dual-probe FISH assay PathVysion was chosen as the 'gold standard' against which pharmDx (dual-probe) and INFORM (mono-probe) FDA-approved FISH kits and the SPoT-Light CISH kit were compared. Tumours were also evaluated by IHC with the FDA-approved HercepTest kit and a validated in-house IHC protocol. Fifty-five patients with invasive breast carcinoma were selected as a representative proportion of HER2 IHC 2+ cases.

Results
HER2 amplification was observed in 31% of tumours by PathVysion compared with 33% with pharmDx. The number of amplified tumours detected by INFORM and CISH varied with the threshold applied. Agreement was excellent between PathVysion and pharmDx (100%), good with SPoT-Light (89%; cutoff at least five signals per nucleus) and moderate with INFORM (76%; cutoff more than four signals per nucleus). Agreement with INFORM improved to 98% with a cutoff of at least six signals per nucleus.

Conclusion
With an appropriate cutoff, the INFORM kit was comparable to dual-probe FISH kits for evaluating HER2 status. We validate and recommend CISH as an appropriate assay for HER2 scoring that is easy to interpret and requires equipment readily found in, or that can be adapted to, all pathology laboratories. For borderline IHC cases, dual-probe FISH analysis remains the most useful protocol to apply.
Donor Lymphocyte Infusion in the Treatment of First Hematological Relapse After Allogeneic Stem-Cell Transplantation in Adults With Acute Myeloid Leukemia: A Retrospective Risk Factors Analysis and Comparison With Other Strategies by the EBMT Acute Leukemia Working Party
Authors: Schmid Christoph , Labopin Myriam , Nagler Arnon , Bornhäuser Martin , Finke Jürgen , Fassas Athanasios , Volin Liisa , Gürman Günham , Maertens Johan , Bordigoni Pierre , Holler Ernst , Ehninger Gerhard , Polge Emmanuelle , Gorin Norbert-Claude , Kolb Hans-Jochem , Rocha Vanderson 
Published: October 2007

Purpose To evaluate the role of donor lymphocyte infusion (DLI) in the treatment of relapsed acute myeloid leukemia (AML) after allogeneic hematopoietic stem cell transplantation (HSCT). Patients and Methods We retrospectively analyzed the data of 399 patients with AML in first hematological relapse after HSCT whose treatment did (n = 171) or did not (n = 228) include DLI. After correction for imbalances and established risk factors, the two groups were compared with respect to overall survival. Further, a detailed analysis of risk factors for survival among DLI recipients was performed. Results Median follow-up was 27 and 40 months, respectively. Estimated survival at 2 years (± standard deviation) was 21% ± 3% for patients receiving DLI and 9% ± 2% for patients not receiving DLI. After adjustment for differences between the groups, better outcome was associated with age younger than 37 years (P = .008), relapse occurring more than 5 months after HSCT (P < .0001), and use of DLI (P = .04). Among DLI recipients, a lower tumor burden at relapse (< 35% of bone marrow blasts; P = .006), female sex (P = .02), favorable cytogenetics (P = .004), and remission at time of DLI (P < .0001) were predictive for survival in a multivariate analysis. Two-year survival was 56% ± 10%, if DLI was performed in remission or with favorable karyotype, and 15% ± 3% if DLI was given in aplasia or with active disease. Conclusion Although further evidence for a graft-versus-leukemia effect by DLI is provided, our results confirm, that the clinical benefit is limited to a minority of patients. Strategies to reduce tumor burden before DLI, as well as alternative treatment options should be investigated in adults with relapsed AML after HSCT.
Skeletal Self-Repair : Stress Fracture Healing by Rapid Formation and Densification of Woven Bone
Authors: Uthgenannt Brian A , Kramer Michael H , Hwu Joyce A , Wopenka Brigitte , Silva Matthew J 
Published: October 2007

Abstract
Stress fractures of varying severity were created using a rat model of skeletal fatigue loading. Periosteal woven bone formed in proportion to the level of bone damage, resulting in the rapid recovery of whole bone strength independent of stress fracture severity.
Introduction: A hard periosteal callus is a hallmark of stress fracture healing. The factors that regulate the formation of this woven bone callus are poorly understood. Our objective was to produce stress fractures of varying severity and to assess the woven bone response and recovery of bone strength.
Materials and Methods: We used the forelimb compression model to create stress fractures of varying severity in 192 adult rats. Forelimbs were loaded in fatigue until the displacement reached 30%, 45%, 65%, or 85% of fracture. The osteogenic responses of loaded and contralateral control ulnas were assessed 7 and 14 days after loading using pQCT, μCT, mechanical testing, histomorphometry, and Raman spectroscopy.
Results: Loading stimulated the formation of periosteal woven bone that was maximal near the ulnar midshaft and transitioned to lamellar bone away from the midshaft. Woven bone area increased in a dose-response manner with increasing fatigue displacement. Whole bone strength was partially recovered at 7 days and fully recovered at 14 days, regardless of initial stress fracture severity. The density of the woven bone increased by 80% from 7 to 14 days, caused in part by a 30% increase in the mineral:collagen ratio of the woven bone tissue.
Conclusions: Functional healing of a stress fracture, as evidenced by recovery of whole bone strength, occurred within 2 wk, regardless of stress fracture severity. Partial recovery of strength in the first week was attributed to the rapid formation of a collar of woven bone that was localized to the site of bone damage and whose size depended on the level of initial damage. Complete recovery of strength in the second week was caused by woven bone densification. For the first time, we showed that woven bone formation occurs as a dose-dependent response after damaging mechanical loading of bone.
Discussing Shiloh: A Conversation Beyond the Book
Authors: Clarke Lane W. 
Published: October 2007

An analysis of what appears initially to be a typical literature circle discussion about the book Shiloh illuminates larger issues of the influence of class and gendered discursive practices. Drawing on critical discourse analysis, the author suggests that the ways these fifth‐grade students enact class and gender roles actually positions them outside of desired literacy behaviors.By understanding how students' language practices are shaped and influenced beyond the text, teachers can help students engage in more productive discussions and can create a more positive classroom environment for learning.
Think‐Aloud Strategy: Metacognitive Development and Monitoring Comprehension in the Middle School Second‐Language Classroom
Authors: McKeown Regina G. , Gentilucci James L. 
Published: October 2007

Twenty‐seven middle school English learners participated in a study to determine the efficacy of the Think‐Aloud Strategy, one of several metacognitive strategies created to help students strategically negotiate appropriate meaning from text. Students were grouped by level of English‐language proficiency and were administered a reading comprehension pretest. They were then taught how to use the Think‐Aloud Strategy and were administered a posttest to assess the strategy's effect on their reading comprehension.Use of the Think‐Aloud Strategy was expected to improve comprehension of expository text among all three groups. However, each group presented different results, with only the intermediate group exhibiting benefits from using the strategy.The findings suggest English learners with varying levels of native‐language proficiency have unique instructional needs in reading. No single reading strategy may exist that will improve comprehension in all English learners.
A Case Study of a High School English‐Language Learner and His Reading
Authors: Cohen James 
Published: October 2007

Mario, an adolescent English‐language learner and struggling reader, participated in a university‐sponsored summer literacy program. After the program, a follow‐up literacy assessment was conducted, and Mario was interviewed about his perceptions of and practices with literacy.The findings of this case study demonstrate the possibility that one‐on‐one tutoring, performing specific activities such as think‐alouds when reading, engaging in sustained silent reading for extended periods each day, writing in dialogue journals, and conducting inquiry projects can all influence the motivation and the reading effectiveness of an adolescent English‐language learner who struggles to read. Although it is not possible to make conclusive assertions that any of these activities are effective for all students, it is clear by that they had a positive influence on Mario as a reader.
Afterword
Authors: ROBBINS BRUCE 
Published: October 2007

Why should we care about genre?Following a hint from Wai Chee Dimock, let us perform a conceptual experiment. Imagine that literature departments were to begin hiring faculty members primarily by their expertise in particular genres instead of (as is usually the case in the larger departments) primarily by their expertise in particular historical periods. Literary study, I hope you will agree, would very soon cease to exist in its present form. This prospect exposes something about literary study in its present form that might after all prove unworthy of being mourned, which is to say of being preserved.
Oligonucleotide microarray analysis of estrogen receptor α-positive postmenopausal breast carcinomas: identification of HRPAP20 and TIMELESS as outstanding candidate markers to predict the response to tamoxifen
Authors: Tozlu-Kara S , Roux V , Andrieu C , Vendrell J , Vacher S , Lazar V , Spyratos F , Tubiana-Hulin M , Cohen P , Dessen P , Lidereau R , Bièche I 
Published: October 2007

AbstractThe estrogen receptor α (ERα) status of breast tumors is used to identify patients who may respond to endocrine agents such as tamoxifen. However, ERα status alone is not perfectly predictive, and there is a pressing need for more reliable markers of endocrine responsiveness. In this aim, we used a two-step strategy. We first screened genes of interest by a pangenomic 44 K oligonucleotide microarray in a series of ten ERα-positive tumors from five tamoxifen-treated postmenopausal patients who relapsed (distant metastasis) and five tamoxifen-treated postmenopausal patients who did not relapse, matched with respect to age, Scarff–Bloom–Richardson grade, lymph node status, and macroscopic tumor size. Genes of interest (n=24) were then investigated in an independent well-characterized series of ERα-positive unilateral invasive primary breast tumors from postmenopausal women who received tamoxifen alone as adjuvant hormone therapy after primary surgery. We identified four genes (HRPAP20, TIMELESS, PTPLB, and MGC29814) for which high mRNA levels were significantly associated with shorter relapse-free survival (log-rank test). We also showed that hormone-regulated proliferation-associated 20 kDa protein (HRPAP20) and TIMELESS are 17β-estradiol-regulated in vitro and are ectopically expressed in OH-Tam-resistant cell lines. In conclusion, these findings point to HRPAP20 and TIMELESS as promising markers of tamoxifen resistance in women with ERα-positive breast tumors.
Identification of regulatory elements in the Cyp19 proximal promoter in rat luteal cells
Authors: Stocco Carlos , Kwintkiewicz Jakub , Cai Zailong 
Published: October 2007

AbstractThe cytochrome P450 aromatase (Cyp19) gene encodes an enzyme of crucial importance in the synthesis of estradiol. Estradiol is luteotropic in the rat. In this species, luteal Cyp19 expression increases progressively during pregnancy and falls before parturition. The mechanisms that control these changes are unknown. Using gel shift assays, we sought to identify the promoter regions that control Cyp19 expression in the rat corpus luteum (CL). The Cyp19 promoter contains a cAMP response element-like sequence (CLS), two nuclear receptor elements half sites (NREs), a GATA binding site, a Yin Yang-1 (YY1) response element, and an activation protein 3 (AP3) binding site. Nuclear extracts were obtained from CL of rats on days 4, 15, and 23 of pregnancy and from the ovaries of immature rats treated with vehicle or a hormone that induces Cyp19 expression in the follicles. CLS was active in immature ovaries but inactive in the CL of pregnant rats, whereas binding to NREs and GATA was observed in both tissues. YY1 was inactive in all samples tested. In the CL, AP3 binding was higher on day 15 of pregnancy when compared with day 4 and day 23 but it was absent in ovaries of immature rats, whereas luteinization increased AP3 binding activity. Mutation of the AP3 site blunted the stimulation of Cyp19 promoter activity in granulosa cells. Our results indicate that CLS is active only in follicles; whereas in the CL, binding to the GATA, NRE, and AP3 sites associates with changes in Cyp19 expression, suggesting that they control Cyp19 promoter activity in luteal cells.