bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multispectral fingerprinting for improved in vivo cell dynamics analysis
Authors: Kulesa Paul M , Teddy Jessica M , Smith Miranda , Alexander Richard , Cooper Cameron HJ , Lansford Rusty , McLennan Rebecca 
Published: September 2010

Abstract
Background
Tracing cell dynamics in the embryo becomes tremendously difficult when cell trajectories cross in space and time and tissue density obscure individual cell borders. Here, we used the chick neural crest (NC) as a model to test multicolor cell labeling and multispectral confocal imaging strategies to overcome these roadblocks.

Results
We found that multicolor nuclear cell labeling and multispectral imaging led to improved resolution of in vivo NC cell identification by providing a unique spectral identity for each cell. NC cell spectral identity allowed for more accurate cell tracking and was consistent during short term time-lapse imaging sessions. Computer model simulations predicted significantly better object counting for increasing cell densities in 3-color compared to 1-color nuclear cell labeling. To better resolve cell contacts, we show that a combination of 2-color membrane and 1-color nuclear cell labeling dramatically improved the semi-automated analysis of NC cell interactions, yet preserved the ability to track cell movements. We also found channel versus lambda scanning of multicolor labeled embryos significantly reduced the time and effort of image acquisition and analysis of large 3D volume data sets.

Conclusions
Our results reveal that multicolor cell labeling and multispectral imaging provide a cellular fingerprint that may uniquely determine a cell's position within the embryo. Together, these methods offer a spectral toolbox to resolve in vivo cell dynamics in unprecedented detail.
Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5
Authors: Paul Debarati , Bridges Susan M , Burgess Shane C , Dandass Yoginder S , Lawrence Mark L 
Published: September 2010

Abstract

Background

Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium capable of utilizing CO (carbon monoxide) and fixing CO2 (carbon dioxide). We previously published the draft genome of this organism and recently submitted the complete genome sequence to GenBank.

Results
The genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5 consists of a 3.74-Mb chromosome and a 133-kb megaplasmid that contains the genes responsible for utilization of carbon monoxide, carbon dioxide, and hydrogen. To our knowledge, this strain is the first one to be sequenced in the genus Oligotropha, the closest fully sequenced relatives being Bradyrhizobium sp. BTAi and USDA110 and Nitrobacter hamburgiensis X14. Analysis of the O. carboxidovorans genome reveals potential links between plasmid-encoded chemolithoautotrophy and chromosomally-encoded lipid metabolism. Comparative analysis of O. carboxidovorans with closely related species revealed differences in metabolic pathways, particularly in carbohydrate and lipid metabolism, as well as transport pathways.

Conclusion

Oligotropha, Bradyrhizobium sp and Nitrobacter hamburgiensis X14 are phylogenetically proximal. Although there is significant conservation of genome organization between the species, there are major differences in many metabolic pathways that reflect the adaptive strategies unique to each species.
Apoptosis-associated microRNAs are modulated in mouse, rat and human neural differentiation
Authors: Aranha Márcia M , Santos Daniela M , Xavier Joana M , Low Walter C , Steer Clifford J , Solá Susana , Rodrigues Cecília MP 
Published: September 2010

Abstract

Background
MicroRNAs (miRs or miRNAs) regulate several biological processes in the cell. However, evidence for miRNAs that control the differentiation program of specific neural cell types has been elusive. Recently, we have shown that apoptosis-associated factors, such as p53 and caspases participate in the differentiation process of mouse neural stem (NS) cells. To identify apoptosis-associated miRNAs that might play a role in neuronal development, we performed global miRNA expression profiling experiments in NS cells. Next, we characterized the expression of proapoptotic miRNAs, including miR-16, let-7a and miR-34a in distinct models of neural differentiation, including mouse embryonic stem cells, PC12 and NT2N cells. In addition, the expression of antiapoptotic miR-19a and 20a was also evaluated.

Results
The expression of miR-16, let-7a and miR-34a was consistently upregulated in neural differentiation models. In contrast, expression of miR-19a and miR-20a was downregulated in mouse NS cell differentiation. Importantly, differential expression of specific apoptosis-related miRNAs was not associated with increased cell death. Overexpression of miR-34a increased the proportion of postmitotic neurons of mouse NS cells.

Conclusions
In conclusion, the identification of miR-16, let-7a and miR-34a, whose expression patterns are conserved in mouse, rat and human neural differentiation, implicates these specific miRNAs in mammalian neuronal development. The results provide new insights into the regulation of neuronal differentiation by apoptosis-associated miRNAs.
Activating Transcription Factor 3 regulates in part the enhanced tumour cell cytotoxicity of the histone deacetylase inhibitor M344 and cisplatin in combination
Authors: St Germain Carly , O'Brien Anna , Dimitroulakos Jim 
Published: September 2010

Abstract

Background
Activating Transcription Factor (ATF) 3 is a key regulator of the cellular integrated stress response whose expression has also been correlated with pro-apoptotic activities in tumour cell models. Combination treatments with chemotherapeutic drugs, such as cisplatin, and histone deacetylase (HDAC) inhibitors have been demonstrated to enhance tumour cell cytotoxicity. We recently demonstrated a role for ATF3 in regulating cisplatin-induced apoptosis and others have shown that HDAC inhibition can also induce cellular stress. In this study, we evaluated the role of ATF3 in regulating the co-operative cytotoxicity of cisplatin in combination with an HDAC inhibitor.

Results
The HDAC inhibitor M344 induced ATF3 expression at the protein and mRNA level in a panel of human derived cancer cell lines as determined by Western blot and quantitative RT-PCR analyses. Combination treatment with M344 and cisplatin lead to increased induction of ATF3 compared with cisplatin alone. Utilizing the MTT cell viability assay, M344 treatments also enhanced the cytotoxic effects of cisplatin in these cancer cell lines. The mechanism of ATF3 induction by M344 was found to be independent of MAPKinase pathways and dependent on ATF4, a known regulator of ATF3 expression. ATF4 heterozygote (+/-) and knock out (-/-) mouse embryonic fibroblast (MEF) as well as chromatin immunoprecipitation (ChIP) assays were utilized in determining the mechanistic induction of ATF3 by M344. We also demonstrated that ATF3 regulates the enhanced cytotoxicity of M344 in combination with cisplatin as evidenced by attenuation of cytotoxicity in shRNAs targeting ATF3 expressing cells.

Conclusion
This study identifies the pro-apoptotic factor, ATF3 as a novel target of M344, as well as a mediator of the co-operative effects of cisplatin and M344 induced tumour cell cytotoxicity.
Expression of glypican 3 in placental site trophoblastic tumor
Authors: Ou-Yang Robin J , Hui Pei , Yang Ximing J , Zynger Debra L 
Published: September 2010

Abstract

Background
Glypican-3 (GPC3) is a membrane-bound heparan sulfate proteoglycan that functions in embryonic cell growth and differentiation and is highly expressed in the placenta. GPC3 is mutated in Simpson-Golabi-Behmel syndrome, which is characterized by tissue overgrowth and an increased risk of embryonal malignancies. GPC3 has also been implicated in sporadic cancer, particularly hepatocellular carcinoma, for which it has been shown to be a useful diagnostic marker. Although GPC3 expression has been studied in non-neoplastic placental tissue, its presence in gestational trophoblastic diseases has not been previously explored. The purpose of this study was to investigate the immunohistochemical expression of GPC3 in placental site trophoblastic tumor (PSTT), a very rare gestational trophoblastic neoplasm which may be morphologically confused with non-trophoblastic tumors, and to assess its possible utility as a diagnostic marker.

Methods
Fifteen cases of PSTT, as well as samples from placental site nodule (PSN) (n = 2), leiomyosarcoma (n = 1), leiomyoma (n = 1), invasive cervical squamous cell carcinoma (n = 7) and endometrial adenocarcinoma (n = 11) were examined. Immunoreactivity was semi-quantitatively evaluated as negative (0, < 5% of cells stained), focally positive (1+, 5-10% of cells stained), positive (2+, 11-50% of cells stained) or diffusely positive (3+, > 50% of cells stained). Staining intensity for each subtype was graded from 0 to 3 and a mean intensity was calculated.

Results
Eighty percent of PSTT (12/15) were immunoreactive for GPC3 (0, 20; 1+, 20%; 2+, 40%; 3+, 20%) with a mean intensity of 1.3. Stronger, predominately cytoplasmic staining was seen in larger multi- and mononucleated cells with smaller mononucleate cells showing weak muddy cytoplasmic staining. Both PSN cases were positive (1+, 50%; 2+, 50%) and two of nine invasive cervical squamous cell carcinomas showed staining (0, 57%; 1+, 29%; 2+, 14%), predominately in a basal distribution. Other uterine tumors and non-neoplastic tissues were negative.

Conclusions
Identification of GPC3 in PSTT and PSN is consistent with the derivation of these lesions from intermediate trophoblasts, which have been described to express GPC3. GPC3 may be a useful adjunct immunohistochemical marker in differentiating PSTT from non-trophoblastic tumors.
LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent prostate cancer
Authors: Romanuik Tammy L , Wang Gang , Morozova Olena , Delaney Allen , Marra Marco A , Sadar Marianne D 
Published: September 2010

Abstract

Background
There is no cure for castration-recurrent prostate cancer (CRPC) and the mechanisms underlying this stage of the disease are unknown.

Methods
We analyzed the transcriptome of human LNCaP prostate cancer cells as they progress to CRPC in vivo using replicate LongSAGE libraries. We refer to these libraries as the LNCaP atlas and compared these gene expression profiles with current suggested models of CRPC.

Results
Three million tags were sequenced using in vivo samples at various stages of hormonal progression to reveal 96 novel genes differentially expressed in CRPC. Thirty-one genes encode proteins that are either secreted or are located at the plasma membrane, 21 genes changed levels of expression in response to androgen, and 8 genes have enriched expression in the prostate. Expression of 26, 6, 12, and 15 genes have previously been linked to prostate cancer, Gleason grade, progression, and metastasis, respectively. Expression profiles of genes in CRPC support a role for the transcriptional activity of the androgen receptor (CCNH, CUEDC2, FLNA, PSMA7), steroid synthesis and metabolism (DHCR24, DHRS7, ELOVL5, HSD17B4, OPRK1), neuroendocrine (ENO2, MAOA, OPRK1, S100A10, TRPM8), and proliferation (GAS5, GNB2L1, MT-ND3, NKX3-1, PCGEM1, PTGFR, STEAP1, TMEM30A), but neither supported nor discounted a role for cell survival genes.

Conclusions
The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC.
Intravenous administration of anti-vascular endothelial growth factor humanized monoclonal antibody bevacizumab improves articular cartilage repair
Authors: Nagai Toshihiro , Sato Masato , Kutsuna Toshiharu , Kokubo Mami , Ebihara Goro , Ohta Naoshi , Mochida Joji 
Published: September 2010

Abstract
Introduction
In this study, we investigate the efficacy of repairing an osteochondral defect in rabbit knee joints by administering bevacizumab, a humanized monoclonal anti-vascular endothelial growth factor (VEGF) antibody.

Methods
An osteochondral defect was created on the patellar groove of 20 Japanese white rabbits that were classified into two recipient groups: group B, administration of bevacizumab (100-mg intravenous injection on the day of surgery and 2 weeks later), and a control group (defect only). Rabbits were killed 1 and 3 months postoperatively. Sections were stained with safranin O. Repair sites were evaluated using the modified O'Driscoll International Cartilage Repair Society grading system. The expression of chondromodulin (ChM)-I and VEGF was evaluated using immunohistochemical analyses.

Results
At 1 month postoperatively, the repair site in group B was filled with cartilaginous tissue. At 3 months, the repair site retained this cartilage phenotype. At 1 month in the controls, the defects were mainly filled with fibrous tissue. At 3 months, the defect was replaced by fibrous tissue and bone. Over the 3-month period, histological scores were significantly higher in group B than in the controls. At 1 month, group B showed intense positive results for ChM-I in the bottom of the repair tissue. VEGF was also identified in the same area. In the controls, no ChM-I was observed in the repair tissue. Conversely, the remodeling hypertrophic chondrocyte layer stained intensely for VEGF.

Conclusions
Intravenous administration of bevacizumab contributes to better repair of articular cartilage in an osteochondral defect model. We suggest the possibility of facilitating articular cartilage repair with anti-VEGF antibody rather than using cultured cells or artificial scaffolds.
An Efficient and Numerically Stable Method for Computing Bounds for the Interval Availability Distribution
Authors: Carrasco Juan A. 
Published: September 2010

This paper is concerned with the computation of the interval availability (proportion of time in a time interval in which the system is up) distribution of a fault-tolerant system modeled by a finite (homogeneous) continuous-time Markov chain (CTMC). General-purpose methods for performing that computation tend to be very expensive when the CTMC and the time interval are large. Based on a previously available method (regenerative transformation) for computing the interval availability complementary distribution, we develop a method called bounding regenerative transformation for the computation of bounds for that measure. Similar to regenerative transformation, bounding regenerative transformation requires the selection of a regenerative state. The method is targeted at a certain class of models, including both exact and bounding failure/repair models of fault-tolerant systems with increasing structure function, with exponential failure and repair time distributions and repair in every state with failed components having failure rates much smaller than repair rates (F/R models), with a “natural” selection for the regenerative state. The method is numerically stable and computes the bounds with well-controlled error. For models in the targeted class and the natural selection for the regenerative state, computational cost should be traded off with bounds tightness through a control parameter. For large models in the class, the version of the method that should have the smallest computational cost should have small computational cost relative to the model size if the value above which the interval availability has to be guaranteed to be is close to 1. In addition, under additional conditions satisfied by F/R models, the bounds obtained with the natural selection for the regenerative state by the version that should have the smallest computational cost seem to be tight for all time intervals or not small time intervals, depending on whether the initial probability distribution of the CTMC is concentrated in the regenerative state or not. CORRECTED VERSION OF RECORD, SEE LAST PAGE OF ARTICLE
Audit of local recurrence following breast conservation surgery with 5-mm target margin and hypofractionated 40-Gray breast radiotherapy for invasive breast cancer
Authors: Liau Siong-Seng , Cariati Massimiliano , Noble David , Wilson Charles , Wishart Gordon C 
Published: September 2010

INTRODUCTION The risk of ipsilateral breast tumour recurrence (IBTR) following breast conservation surgery (BCS) for invasive breast cancer (IBC) and radiotherapy is dependent on patient-, tumour- and treatment-related variables. In the Cambridge Breast Unit, breast conserving surgery has been performed with a target radial margin of 5 mm for IBC, in combination with 40-Gy hypofractionated (15 fractions) breast radiotherapy, since 1999. PATIENTS AND METHODS An audit was performed of cases treated between 1999 and 2004. A total of 563 patients underwent BCS for invasive breast cancer with 90.4% receiving radiotherapy (RT) and 60.4% of patients receiving boost RT (3 fractions of 3-Gy). RESULTS After a median follow-up of 58 months, five of the 563 (0.9%) patients developed IBTR. The 5-year actuarial IBTR rate was 1.1%. In terms of distant disease recurrence (DDR), 29 of the 563 (5.2%) had DDR during follow-up, giving a 5-year actuarial DDR rate of 5.4%. The 5-year breast cancer specific survival was 95%, with the poorer NPI groups having worse breast cancer specific survival (Log-rank, P < 0.0001). More importantly, patients with IBTR had a shorter breast cancer-specific survival than those who were IBTR-free (Log-rank, P < 0.0001). CONCLUSIONS Our treatment regimen, combining BCS with a 5-mm target margin and hypofractionated 40-Gy RT, results in an extremely low rate of IBTR, and compares favourably with the target IBTR rate of < 5% defined by the Association of Breast Surgeons (ABS) at BASO guidelines.
Four-part proximal humeral fractures: diagnosis with the ‘sunset’ sign on anteroposterior radiograph
Authors: Kachramanoglou C , Chidambaram R , Mok D 
Published: September 2010

INTRODUCTION Four-part proximal humeral fractures require surgical intervention. However, they can be difficult to diagnose in radiological images. We aim to define a new, easily recognisable, radiological sign as a predictor of four-part fracture of the proximal humerus in a plain anteroposterior radiograph of the shoulder. PATIENTS AND METHODS We describe our ‘sunset’ sign as ‘articular surface of humeral head pointing away from the glenoid and tilted upwards, in the presence of a displaced greater tuberosity fracture’. We postulate that a patient with proximal humerus fracture showing this sign has four-part fracture until proven otherwise. Between 2002 and 2006, 80 consecutive patients had surgical treatment of their proximal humeral fractures in our unit. Pre-operative radiographs and operative notes of 79 patients were evaluated independently by three blinded observers. The presence of ‘sunset’ sign was recorded. Findings were then correlated with the operative diagnoses to confirm whether they were four-part fractures or not. With 95% confidence interval, we calculated the sensitivity, specificity, positive and negative predictive values for our diagnostic sign. RESULTS Of 79 patients, 30 displayed ‘sunset’ sign in their pre-operative radiograph. Of these, 28 had confirmed four-part fractures operatively. The positive predictive value of ‘sunset’ sign was 93%. The specificity and sensitivity were 95% and 78%, respectively. The sensitivity was affected by eight patients with four-part fractures with displaced articular head fragment which had dropped either medially or posteriorly. CONCLUSIONS These results suggest that, in patients with proximal humeral fractures, the presence of ‘sunset’ sign in the anteroposterior radiograph is a reliable indicator of four-part fracture.
Acupuncture therapy for chronic lower back pain: a systematic review
Authors: Trigkilidas Dionysios 
Published: September 2010

INTRODUCTION Chronic low back pain is a common condition affecting a significant proportion of the population and has large economic implications on the society. Acupuncture has grown in popularity as an alternative therapy for chronic low back pain. Recent National Institute for Health and Clinical Excellence (NICE) guidelines on low back pain offer a course of acupuncture as a baseline treatment option according to patient preference. The aim of this systematic review was to evaluate if this treatment option is justified in view of recent evidence available on the efficacy of acupuncture. MATERIALS AND METHODS Studies included were identified by a PubMed search for relevant, randomised, controlled trials on the 23 July 2009. A systematic review was performed. RESULTS Fifteen randomised controlled trials were identified. Of these, four met the eligibility criteria and were critically appraised. These trials suggest acupuncture can be superior to usual care in treating chronic low back pain, especially, when patients have positive expectations about acupuncture. CONCLUSIONS NICE guidelines of a course of acupuncture, offered according to patient preference as a treatment option for chronic low back pain, are justified.
Short course pre-operative ferrous sulphate supplementation – is it worthwhile in patients with colorectal cancer?
Authors: Quinn Martha , Drummond Robert J , Ross Fiona , Murray Juliette , Murphy John , Macdonald Angus 
Published: September 2010

INTRODUCTION Pre-operative anaemia is well recognised in patients presenting with colorectal cancer (CRC). While the benefits of long-term FeSO4 supplementation on Fe deficiency anaemia are well established, it is not known if short-course supplementation (2–3 weeks) impacts significantly on pre-operative haemoglobin (Hb) levels. This study examines the impact of short-term, oral FeSO4 supplementation on patients undergoing surgery for CRC. PATIENTS AND METHODS All patients with CRC presenting to a single surgeon were included. At diagnosis, baseline Hb and blood film were checked on all patients who then received 200 mg tds of FeSO4. Haemoglobin was rechecked pre-operatively and daily postoperatively. Patients requiring pre-operative blood transfusions were excluded from analysis. RESULTS Between 1 January 2004 and 31 December 2006, 117 patients were identified, 14 of whom were excluded. Patients received a median of 39 days’ treatment with FeSO4. Fifty-eight (56.3%) patients were anaemic at presentation gaining a mean of 1.73 g/dl (P < 0.001) from short-course FeSO4 supplementation. Right-sided tumours (lower mean Hb at presentation; P = 0.008) responded more to FeSO4 when compared to left-sided tumours (P < 0.017). Increase in Hb was unrelated to pathological stage. The transfusion rate for all curative resections was 0.69 units/patient. For the historical cohort (patients undergoing curative resection between 1 January 2001 and 31 December 2003), the mean transfusion rate fell from 1.69 units/patient. CONCLUSIONS Routine short-course supplementation with iron offers improved pre-operative Hb prior to surgery in CRC, especially in right-sided lesions and those with presenting anaemia.