bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria
Authors: González Pérez Abel D , González González Evelyn , Espinosa Angarica Vladimir , Vasconcelos Ana Tereza R , Collado-Vides Julio 
Published: August 2009

Abstract

Background
In the past years, several studies begun to unravel the structure, dynamical properties, and evolution of transcriptional regulatory networks. However, even those comparative studies that focus on a group of closely related organisms are limited by the rather scarce knowledge on regulatory interactions outside a few model organisms, such as E. coli among the prokaryotes.

Results
In this paper we used the information annotated in Tractor_DB (a database of regulatory networks in gamma-proteobacteria) to calculate a normalized Site Orthology Score (SOS) that quantifies the conservation of a regulatory link across thirty genomes of this subclass. Then we used this SOS to assess how regulatory connections have evolved in this group, and how the variation of basic regulatory connection is reflected on the structure of the chromosome. We found that individual regulatory interactions shift between different organisms, a process that may be described as rewiring the network. At this evolutionary scale (the gamma-proteobacteria subclass) this rewiring process may be an important source of variation of regulatory incoming interactions for individual networks. We also noticed that the regulatory links that form feed forward motifs are conserved in a better correlated manner than triads of random regulatory interactions or pairs of co-regulated genes. Furthermore, the rewiring process that takes place at the most basic level of the regulatory network may be linked to rearrangements of genetic material within bacterial chromosomes, which change the structure of Transcription Units and therefore the regulatory connections between Transcription Factors and structural genes.

Conclusion
The rearrangements that occur in bacterial chromosomes-mostly inversion or horizontal gene transfer events – are important sources of variation of gene regulation at this evolutionary scale.
Bioluminescence-based visualization of CD4 T cell dynamics using a T lineage-specific luciferase transgenic model1
Authors: Chewning Joseph H , Dugger Kari J , Chaudhuri Tandra R , Zinn Kurt R , Weaver Casey T 
Published: August 2009

AbstractBackgroundRapid clonal expansion of T cells occurs in response to antigenic challenges. The kinetics of the T cell response has previously been described using tissue-based studies performed at defined time points. Luciferase bioluminescence has recently been utilized for non-invasive analysis ofin vivobiologic processes in real-time.ResultsWe have created a novel transgenic mouse model (T-Lux) using a human CD2 mini-gene to direct luciferase expression specifically to the T cell compartment. T-Lux T cells demonstrated normal homing patterns within the intact mouse and following adoptive transfer. Bioluminescent signal correlated with T cell numbers in the whole body images as well as within specific organ regions of interest. Following transfer into lymphopenic (RAG2-/-) recipients, homeostatic proliferation of T-Lux T cells was visualized using bioluminescent imaging. Real-time bioluminescent analysis of CD4+T cell antigen-specific responses enabled real-time comparison of the kinetics and magnitude of clonal expansion and contraction in the inductive lymph node and tissue site of antigen injection. T cell expansion was dose-dependent despite the presence of supraphysiologic numbers of OVA-specific OT-II transgenic TCR T-Lux T cells. CD4+T cells subsequently underwent a rapid (3–4 day) contraction phase in the draining lymph node, with a delayed contraction in the antigen delivery site, with bioluminescent signal diminished below initial levels, representing TCR clonal frequency control.ConclusionThe T-Lux mouse provides a novel, efficient model for trackingin vivoaspects of the CD4+T cell response to antigen, providing an attractive approach for studies directed at immunotherapy or vaccine design.
Confocal Microscopy of Unfixed Breast Needle Core Biopsies: A Comparison to Fixed and Stained Sections
Authors: Schiffhauer Linda M , Boger J Neil , Bonfiglio Thomas A , Zavislan James M , Zuley Margarita , Fox Christi Alessi 
Published: August 2009

AbstractBackgroundNeedle core biopsy, often in conjunction with ultrasonic or stereotactic guided techniques, is frequently used to diagnose breast carcinoma in women. Confocal scanning laser microscopy (CSLM) is a technology that provides real-time digital images of tissues with cellular resolution. This paper reports the progress in developing techniques to rapidly screen needle core breast biopsy and surgical specimens at the point of care. CSLM requires minimal tissue processing and has the potential to reduce the time from excision to diagnosis. Following imaging, specimens can still be submitted for standard histopathological preparation.MethodsNeedle core breast specimens from 49 patients were imaged at the time of biopsy. These lesions had been characterized under the Breast Imaging Reporting And Data System (BI-RADS) as category 3, 4 or 5. The core biopsies were imaged with the CSLM before fixation. Samples were treated with 5% citric acid and glycerin USP to enhance nuclear visibility in the reflectance confocal images. Immediately following imaging, the specimens were fixed in buffered formalin and submitted for histological processing and pathological diagnosis. CSLM images were then compared to the standard histology.ResultsThe pathologic diagnoses by standard histology were 7 invasive ductal carcinomas, 2 invasive lobular carcinomas, 3 ductal carcinomas in-situ (CIS), 21 fibrocystic changes/proliferative conditions, 9 fibroadenomas, and 5 other/benign; two were excluded due to imaging difficulties. Morphologic and cellular features of benign and cancerous lesions were identified in the confocal images and were comparable to standard histologic sections of the same tissue.ConclusionCSLM is a technique with the potential to screen needle core biopsy specimens in real-time. The confocal images contained sufficient information to identify stromal reactions such as fibrosis and cellular proliferations such as intra-ductal and infiltrating carcinoma, and were comparable to standard histologic sections of the same tissue. Morphologic and cellular features of benign and cancerous lesions were identified in the confocal images. Additional studies are needed to 1.) establish correlation of the confocal and traditional histologic images for the various diseases of the breast; 2.) validate diagnostic use of CSLM and; 3.) further define features of borderline lesions such as well-differentiated ductal CIS vs. atypical hyperplasia.
Sequence variation of PfEMP1-DBLα in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria
Authors: Horata Natharinee , Kalambaheti Thareerat , Craig Alister , Khusmith Srisin 
Published: August 2009

AbstractBackgroundRosetting and cytoadherence ofPlasmodium falciparum-infected red blood cells have been associated with severity of malaria. ICAM-1 and CD36 are the main host cell receptors, while PfEMP1-DBLα is a major parasite ligand, which can contribute to rosette formation. This study is aimed at demonstrating whether the highly polymorphic PfEMP1-DBLα sequences occurring among Thai isolates causing severe and uncomplicated malaria are associated with their ability to form rosettes and reflected the clinical outcome of the patients.MethodsTwo hundred and ninety five PfEMP1-DBLα sequences from Thai clinical isolates causing severe and uncomplicated malaria were evaluated by sequencing and direct comparison using the specific text string analysis functions in Microsoft Excel and Perl. The relationships between the PfEMP1-DBLα sequences were also analysed by network analysis. The binding abilities of parasitized red blood cells (PRBCs) to CD36, wild type ICAM-1, ICAM-1Kilifiand ICAM-1S22/Aunder static condition were included.ResultsTwo hundred and eighty one non-identical amino acid sequences were identified (< 95% sequence identity). When the distributions of semi-conserved features (PoLV1–4 and sequence group) within the rosetting domain PfEMP1-DBLα were observed, close similarity was found between isolates from the two disease groups. The sequence group 1 representing uncomplicated malaria was significantly different from the sequence group 3 representing the majority of severe malaria (p= 0.027). By using a simple non-phylogenetic approach to visualize the sharing of polymorphic blocks (position specific polymorphic block, PSPB) and cys/PoLV among DBLα sequences, the sequence group 1 was split from the other five sequence groups. The isolates belonging to sequence group 5 gave the highest mean rosetting rate (21.31%). However, within sequence group 2 and group 6, the isolates causing severe malaria had significantly higher rosetting rate than those causing uncomplicated malaria (p= 0.014,p= 0.007, respectively).ConclusionThis is the first report of PfEMP1-DBLα analysis in clinical Thai isolates using semi-conserved features (cys/PoLV and PSPBs). The cys/PoLV group 5 gave the highest rosetting rate. PfEMP1-DBLα domains in Thai isolates are highly diverse, however, clinical isolates from severe and uncomplicated malaria shared common sequences.
The complete genomic sequence of an in vivo low replicating BLV strain
Authors: Dube Syamalima , Abbott Lynn , Dube Dipak K , Dolcini Guillermina , Gutierrez Silvina , Ceriani Carolina , Juliarena Marcela , Ferrer Jorge , Perzova Raisa , Poiesz Bernard J 
Published: August 2009

Abstract
DNA was extracted from lamb lymphocytes that were infected in vivo with a BLV strain after inoculation with the peripheral blood mononuclear cells from a persistently sero-indeterminate, low viral load, BLV-infected Holstein cow (No. 41) from Argentina. The DNA was PCR amplified with a series of overlapping primers encompassing the entire BLV proviral DNA. The amplified BLV ARG 41 DNA was cloned, sequenced, and compared phylogenetically to other BLV sequences including an in vivo high replicating strain (BLV ARG 38) from the same herd in Argentina. Characterization of BLV ARG 41's deduced proteins and its relationship to other members of the PTLV/BLV genus of retroviruses are discussed.
Municipal policies and plans of action aiming to promote physical activity and healthy eating habits among schoolchildren in Stockholm, Sweden: a cross-sectional study
Authors: Guldbrandsson Karin , Wennerstad Karin Modig , Rasmussen Finn 
Published: August 2009

Abstract

Background
Promoting physical activity and healthy eating habits by structural measures that reach most children in a society is presumably the most sustainable way of preventing development of overweight and obesity in childhood. The main purpose of the present study was to analyse whether policies and plans of action at the central level in municipalities increased the number of measures that aim to promote physical activity and healthy eating habits among schoolchildren aged six to 16. Another purpose was to analyse whether demographic and socio-economic characteristics were associated with the level of such measures.

Methods
Questionnaires were used to collect data from 25 municipalities and 18 town districts in Stockholm County, Sweden. The questions were developed to capture municipal structural work and factors facilitating physical activity and the development of healthy eating habits for children. Local policy documents and plans of action were gathered. Information regarding municipal demographic and socio-economic characteristics was collected from public statistics.

Results
Policy documents and plans of action in municipalities and town districts did not seem to influence the number of measures aiming to promote physical activity and healthy eating habits among schoolchildren in Stockholm County. Municipal demographic and socio-economic characteristics were, however, shown to influence the number of measures. In town districts with a high total population size, and in municipalities and town districts with a high proportion of adults with more than 12 years of education, a higher level of health-promoting measures was found. In municipalities with a high annual population growth, the number of measures was lower than in municipalities with a lower annual population growth. Another key finding was the lack of agreement between what was reported in the questionnaires regarding existence and contents of local policies and plans of action and what was actually found when these documents were scrutinized.

Conclusion
Policy documents and plans of action aiming to promote physical activity and healthy eating habits among schoolchildren aged six to 16 in municipalities and town districts in Stockholm County did not seem to have an impact on the local level of measures. Demographic and socio-economic characteristics of the municipalities and town districts were on the other hand associated with local health-promoting measures.
Establishment of an animal model of a pasteurized bone graft, with a preliminary analysis of muscle coverage or FGF-2 administration to the graft
Authors: Yoshida Tatsuya , Sakamoto Akio , Tsukamoto Nobuaki , Nakayama Koichi , Iwamoto Yukihide 
Published: August 2009

Abstract

Background
Pasteurized bone grafting is used following the excision of a bone tumor for the purpose of eliminating neoplastic cells while preserving bone-inducing ability. In the hopes of guaranteeing the most favourable results, the establishment of an animal model has been urgently awaited. In the course of establishing such a model, we made a preliminary examination of the effect of muscle coverage or fibroblast growth factor 2 (FGF-2) administration radiographically.

Methods
Forty pasteurized intercalary bone grafts of the Wistar rat femur treated at 60°C for 30 min were reimplanted and stabilized with an intramedullary nail (1.1 mm in diameter). Some grafts were not covered by muscle after the implantation, so that they could act as a clinical model for wide resection, and/or these were soaked with FGF-2 solution prior to implantation. The grafts were then divided into 3 groups, comprising 12 grafts with muscle-covering but without FGF-2 (MC+; FGF2-), 12 grafts without muscle-covering and without FGF-2 (MC-; FGF2-) and 16 grafts without muscle covering but with FGF-2 (MC-; FGF2+).

Results
At 2 weeks after grafting, the pasteurized bone model seemed to be successful in terms of eliminating living cells, including osteocytes. At 4 weeks after grafting, partial bone incorporation was observed in half the (MC+; FGF2-) cases and in half the (MC-; FGF2+) cases, but not in any of the (MC-; FGF2-) cases. At 12 weeks after grafting, bone incorporation was seen in 3 out of 4 in the (MC+; FGF2-) group (3/4: 75%) and in 3 out of 8 in the (MC-; FGF2+) group (3/8: 38%). However, most of the grafted bones without FGF-2 were absorbed in all the cases, massively, regardless of whether there had been muscle-covering (MC+; FGF2-; 4/4: 100%) or no muscle-covering (MC-; FGF2-; 4/4: 100%), while bone absorption was noted at a lower frequency (2/8: 25%) and to a lower degree in the (MC-; FGF2+) group.

Conclusion
In conclusion, we have established an animal pasteurized bone graft model in rats. Pasteurized bone was able to maintain bone induction ability. Despite the low number of cases in each group, the results of each group suggest that muscle-covering has an effect on bone incorporation, but that it is not able to prevent bone absorption to the pasteurized bone. However, an application of FGF-2 may have a positive effect on bone incorporation and may be able to prevent bone absorption of the graft in cases of pasteurized bone graft.
Unconventional antigen-presenting cells in the induction of peripheral CD8+ T cell tolerance
Authors: Reynoso Erika D , Turley Shannon J 
Published: August 2009

Abstract
This review highlights the role of nonhematopoietic cells in the induction and maintenance of peripheral CD8+ T cell tolerance.
Bone marrow-derived APCs are considered the predominant cell type involved in the induction and maintenance of T cell tolerance in vivo. In the periphery, cross-presentation of self-antigens by DCs, in particular, CD8α+ DCs, has been the most discussed mechanism underlying the induction of CD8+ T cell tolerance against self. However, nonhematopoietic APCs in the liver, skin, parenchymal tissues, and lymph nodes can also present self- and exogenous antigens to CD8+ T cells under steady-state conditions. Although far surpassed by their DC counterparts in their ability to stimulate T cell responses, these unconventional APCs have been shown to play a role in the induction, maintenance, and regulation of peripheral CD8+ T cell tolerance by a multitude of mechanisms. In this review, we will discuss the different nonhematopoietic cells that have been shown to present tissue-specific or exogenous antigens to naïve CD8+ T cells, thereby contributing to the regulation of T cell responses in the periphery.
Phase II Study of Clofarabine in Pediatric Patients With Refractory or Relapsed Acute Myeloid Leukemia
Authors: Jeha Sima , Razzouk Bassem , Rytting Michael , Rheingold Susan , Albano Edythe , Kadota Richard , Luchtman-Jones Lori , Bomgaars Lisa , Gaynon Paul , Goldman Stewart , Ritchey Kim , Arceci Robert , Altman Arnold , Stine Kimo , Steinherz Laurel , Steinherz Peter 
Published: August 2009

Purpose To determine the efficacy and safety of clofarabine in pediatric patients with refractory or relapsed acute myeloid leukemia (AML). Patients and Methods A phase II, open-label, multicenter study was conducted with single-agent clofarabine in pediatric patients with refractory or relapsed AML. Clofarabine was administered intravenously over 2 hours at the pediatric maximum-tolerated dose (MTD) of 52 mg/m2 daily for 5 consecutive days. Cycles were repeated every 2 to 6 weeks. Responses determined by an independent response review panel. Results The 42 patients treated on the study had a median age of 13 years (range, 2 to 22 years) and had received a median number of two (range, one to five) prior regimens. The response rate was 26% and included one complete response without platelet recovery and 10 partial responses. The median duration of response was 20 weeks (range, 2 to ≥ 156 weeks). Six of 28 patients who were refractory to the immediately preceding therapy achieved response. Thirteen patients (31%), including seven responders, proceeded to hematopoietic stem-cell transplantation (HSCT) after treatment with clofarabine and survived between 24 to ≥ 160 weeks. Five patients (12%) remain alive post-transplantation at ≥ 63, ≥ 71, ≥ 86, ≥ 114, and ≥ 130 weeks. The most common grade 3 or greater adverse events without regard to causality were febrile neutropenia, catheter-related infection, epistaxis, hypotension, nausea, and fever. Transient elevation of liver enzymes and hypokalemia occurred frequently. Five patients died within 30 days of clofarabine administration secondary to progressive disease, and another five died as a result of an adverse event. Conclusion Clofarabine is active in pediatric patients with multiply relapsed or refractory AML. Responses allowed several refractory patients to proceed to HSCT. The toxicity profile was expected in this patient population.
Quality of Surveillance for Stage I Testis Cancer in the Community
Authors: Yu Hua-yin , Madison Rodger A. , Setodji Claude M. , Saigal Christopher S. 
Published: August 2009

Purpose Patients with clinical stage I testicular germ cell tumors have been managed with adjuvant radiotherapy, chemotherapy, or retroperitoneal lymph node dissection (RPLND). The use of surveillance-only strategies at referral centers has yielded survival outcomes comparable to those achieved with adjuvant therapy. We evaluated compliance with follow-up protocols developed at referral centers within the community. Methods We identified patients with stage I testis cancer within a large private insurance claims database and calculated compliance of follow-up test use with guidelines from the National Comprehensive Cancer Network. Results Surveillance was widely used in the community. Compliance with surveillance and postadjuvant therapy follow-up testing was poor and degraded with increasing time from diagnosis. Nearly 30% of all surveillance patients received no abdominal imaging, chest imaging, or tumor marker tests within the first year of diagnosis. Patients who elected RPLND were most compliant with recommended follow-up testing within the first year. Recurrence rates were consistent with previously reported literature, despite poor compliance. Conclusion Surveillance is a widely accepted strategy in clinical stage I testicular cancer treatment in the community. However, follow-up care recommendations developed at referral centers are not being adhered to in the community. Although recurrence rates are similar to those of reported literature, the clinical impact of noncompliance on recurrence severity and mortality are not known. Further prospective work needs to be done to evaluate this apparent quality of care problem in the community.
Prospective Study of [18F]Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography for Staging of Muscle-Invasive Bladder Carcinoma
Authors: Kibel Adam S. , Dehdashti Farrokh , Katz Matthew D. , Klim Aleksandra P. , Grubb Robert L. , Humphrey Peter A. , Siegel Cary , Cao Dengfeng , Gao Feng , Siegel Barry A. 
Published: August 2009

Purpose Novel imaging modalities are needed to detect occult metastatic disease in bladder carcinoma. Patients with regional lymphatic spread could be targeted for neoadjuvant chemotherapy, and patients with distant metastatic disease could be spared the unnecessary morbidity of radical cystectomy. Herein, we report a prospective study of positron emission tomography/computed tomography (PET/CT) with [18F]fluorodeoxyglucose (FDG) in patients undergoing radical cystectomy for cT2-3N0M0 urothelial carcinoma of the bladder. Methods Forty-three chemotherapy-naïve patients underwent FDG-PET/CT before planned cystectomy. All had negative conventional CT and bone scintigraphy before enrollment. Positive FDG-PET/CT was confirmed by percutaneous biopsy or open surgical exploration, whereas negative FDG-PET/CT was confirmed by complete lymphadenectomy. Recurrence-free survival (RFS), disease-specific survival (DSS), and overall survival (OS) were described using the Kaplan-Meier method and compared using log-rank test. Results Median follow-up was 14.9 months (range, 0.4 to 46.1 months). One patient who did not undergo lymphadenectomy was excluded from the pathology data analysis (n = 42), whereas another patient who failed to return for follow-up was excluded from survival analysis (n = 42). FDG-PET/CT demonstrated a positive predictive value of 78% (seven of nine), a negative predictive value of 91% (30 of 33), sensitivity of 70% (seven of 10), and specificity of 94% (30 of 32). RFS, DSS, and OS were all significantly poorer in the patients with positive FDG-PET/CT than in those with negative FDG-PET/CT. Conclusion FDG-PET/CT detected occult metastatic disease in seven of 42 patients with negative conventional preoperative evaluations. PET findings were strongly correlated with survival. As such, FDG-PET/CT may help in making treatment decisions before radical cystectomy.