bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple and novel method for RNA‐seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase
Authors: Brouilette Scott , Kuersten Scott , Mein Charles , Bozek Monika , Terry Anna , Dias Kerith‐Rae , Bhaw‐Rosun Leena , Shintani Yasunori , Coppen Steven , Ikebe Chiho , Sawhney Vinit , Campbell Niall , Kaneko Masahiro , Tano Nobuko , Ishida Hidekazu , Suzuki Ken , Yashiro Kenta 
Published: August 2012

AbstractBackground: Deep sequencing of single cell‐derived cDNAs offers novel insights into oncogenesis and embryogenesis. However, traditional library preparation for RNA‐seq analysis requires multiple steps with consequent sample loss and stochastic variation at each step significantly affecting output. Thus, a simpler and better protocol is desirable. The recently developed hyperactive Tn5‐mediated library preparation, which brings high quality libraries, is likely one of the solutions. Results and Conclusions: Here, we tested the applicability of hyperactive Tn5‐mediated library preparation to deep sequencing of single cell cDNA, optimized the protocol, and compared it with the conventional method based on sonication. This new technique does not require any expensive or special equipment, which secures wider availability. A library was constructed from only 100 ng of cDNA, which enables the saving of precious specimens. Only a few steps of robust enzymatic reaction resulted in saved time, enabling more specimens to be prepared at once, and with a more reproducible size distribution among the different specimens. The obtained RNA‐seq results were comparable to the conventional method. Thus, this Tn5‐mediated preparation is applicable for anyone who aims to carry out deep sequencing for single cell cDNAs. Developmental Dynamics 241:1584–1590, 2012. © 2012 Wiley Periodicals Inc.
Analysis of Amyloid Beta Aggregation Kinetics Using Sym‐Triazine β‐Sheet Inhibitors
Authors: Veloso Anthony J. , Hung Vinci W. S. , Cheng Xin R. , Kerman Kagan 
Published: August 2012

AbstractAD (Alzheimer’s disease) is a progressive neurodegenerative disorder characterized by the cerebral accumulation of fibrillar amyloid‐beta (Aβ) aggregates. Here we present the electrochemistry of two novel sym‐triazine derivatives (TAE‐1, TAE‐2) as modulators of Aβ1–42 aggregation in vitro. Incubation studies conducted at physiological conditions demonstrated strong inhibition of β‐sheet fibril formation. Uniquely, square‐wave voltammetry indicated progressive changes in the surface‐availability of amyloid‐intercalated triazines for oxidation, mediated by competing peptide self‐assembly. Time‐resolved voltammetric analysis showed increasing anodic peak currents (≥3‐fold) and progressive shifts in redox potentials, measured over 24 h. The more potent aggregation modulator (TAE‐2) showed prolonged association during the pre‐nucleation states of Aβ.
Fate and effects of acetyl cedrene in sediments inhabited by different densities of the deposit feeder, Capitella teleta
Authors: Dai Lina , Selck Henriette , Salvito Daniel , Forbes Valery E. 
Published: August 2012

Abstract
Fragrance materials, such as acetyl cedrene (AC), are of environmental concern because they are continuously released to aquatic systems down the drain. In the present study, Capitella teleta (formerly Capitella capitata species I) was exposed to AC-amended sediment at two population densities corresponding to 44,000 and 88,000 worms/m2. The fate of AC in systems with worms was compared to that in identical systems without worms. We examined the toxicity of AC on worm survival, growth, and feeding rate, and quantified the fate of AC in exposure systems by mass balance. Worm survival was close to 100% in all treatments. Acetyl cedrene had some positive effects on worm growth, but not feeding, whereas density had negative effects on both growth and feeding rates. After 14 d, the sediment concentration of AC was reduced by 88 to 99% in the presence of worms, whereas sediment AC concentration was reduced by 13 to 31% or less in the absence of worms. Acetyl cedrene was detected in fecal pellets, at low concentrations compared to the initial concentration in the sediment, but not in worm tissue, suggesting that ingested AC is bioavailable to Capitella teleta and that worms can biotransform sediment-associated AC effectively. Environ. Toxicol. Chem. 2012; 31: 2639–2646. © 2012 SETAC
Airway management after maxillectomy with free flap reconstruction
Authors: Brickman Daniel S. , Reh Douglas D. , Schneider Daniel S. , Bush Ben , Rosenthal Eben L. , Wax Mark K. 
Published: August 2012

AbstractBackgroundMaxillectomy defects require complex 3‐dimensional reconstructions often best suited to microvascular free tissue transfer. Postoperative airway management during this procedure has little discussion in the literature and is often dictated by surgical dogma. The purpose of this article was to review our experience in order to evaluate the effect of airway management on perioperative outcomes in patients undergoing maxillectomy with free flap reconstruction.MethodsA retrospective chart review was performed on patients receiving maxillectomy with microvascular reconstruction at 2 institutions between 1999 and 2011. Patient's airways were managed with or without elective tracheotomy at the surgical team's discretion and different perioperative outcomes were measured. The primary outcome was incidence of airway complication including pneumonia and need for further airway intervention. Secondary outcome was measured as factors leading to perioperative performance of the tracheotomy.ResultsSeventy‐nine of 143 patients received elective tracheotomy perioperatively. The incidence of airway complication was equivalent between groups (10.1% vs 9.4%; p = .89). Patients with cardiopulmonary comorbidities were more likely to receive perioperative tracheotomy (74.1% vs 50.9%; p = .03) without a difference in airway complications. Other patient cofactors did not have an impact on perioperative tracheotomy or airway complication rate.ConclusionsElective tracheotomy may safely be avoided in a subset of patients undergoing maxillectomy with microvascular reconstruction. Elective tracheotomy should be considered in patients with cardiopulmonary risk factors. Head Neck, 2013
Aggressive fibromatosis in the head and neck region: Benign tumor with often mutilating effects
Authors: Hendriks Mathijs P. , Driessen Chantal M. L. , van Laarhoven Hanneke W. M. , Janssens Geert O. R. J. , Verbist Berit M. , van der Graaf Winette T. A. , Slootweg Piet J. , Merkx Matthias A. W. , van Herpen Carla M. L. 
Published: August 2012

AbstractBackgroundAggressive fibromatosis (AF) or desmoid tumor of the head and neck region is a rare, usually unresectable, benign soft tissue tumor with locally aggressive behavior.Methods and ResultsA 31‐year‐old woman presented with a progressive trismus, a swelling in the retromandibular area, as well as loss of sensibility of the maxillary and mandibular branch of the trigeminal nerve. MRI of the head and neck revealed an infiltrative mass involving the masticator, parapharyngeal, and prevertebral and paravertebral space on the left with intracranial extension through the orbital fissure. After the fifth biopsy, 15 months after presentation, the diagnosis of AF was made. The tumor was unresectable, so intensity‐modulated radiotherapy was given with curative intent using a total dose of 60 Gy in 30 fractions of 2 Gy. After 16 months, she showed progressive disease, for which tamoxifen 40 mg twice daily was started with a good response for 2 years. After that, she started with sorafinib, on which she has stable disease now.ConclusionThe often long delay in proper diagnosis and the treatment challenges of a desmoid tumor are illustrated in this case. Furthermore, this article reviews the literature concerning AF, especially of the head and neck region. Head Neck, 2013
Angiogenesis and lymphangiogenesis in early‐stage laryngeal carcinoma: Prognostic implications
Authors: Bolzoni Villaret Andrea , Barbieri Diego , Peretti Giorgio , Schreiber Alberto , Fisogni Simona , Lonardi Silvia , Facchetti Fabio , Nicolai Piero 
Published: August 2012

AbstractBackgroundMany studies have recently emphasized the role of tumor angiogenesis and lymphangiogenesis in regional and distant spread of disease. Although early laryngeal cancer has a favorable oncologic outcome after conservative surgery or radiation therapy, we observed few cases with poor prognosis in terms of locoregional relapse, organ preservation, and survival. The aim of our study was to evaluate the immunohistochemical expression of CD31 and podoplanin to define angiogenic and lymphangiogenic patterns and their possible prognostic implications in previously untreated T1–T2 glottic squamous cell carcinoma.MethodsFour hundred twenty‐eight patients with previously untreated early‐stage laryngeal cancer underwent a laser surgical resection in the period between January 1994 and December 2007. Twenty‐seven cases with poor outcome were identified and compared with a selected sample of 28 patients. All specimens were negative for the presence of high‐risk human papillomavirus genotypes. Patients were followed up until death or for at least 24 months after treatment. Three‐micrometer sections were obtained from formalin‐fixed and paraffin‐embedded tumoral tissues, and an immunohistochemical evaluation was performed. Monoclonal antibodies against CD31 and podoplanin were used for the detection of blood and lymphatic vessels, respectively. A morphometric measurement was used for the analysis of angiogenesis whereas lymphangiogenesis was studied with a semiquantitative technique. The data were analyzed by use of chi‐square and Mann‐Whitney tests as appropriate.ResultsAn increased tumor angiogenesis correlated with local relapse (p = .01), locoregional relapse (p = .01), and death of disease (p = .03). The presence of lymphatic vessels in peritumoral fields had an impact on local (p = .004) and locoregional recurrence (p = .01).ConclusionsEvaluation of angiogenesis and lymphangiogenesis in early‐stage laryngeal cancer could be useful to identify patients at higher risk of recurrence and consequently to modulate treatment planning and follow‐up strategy. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Paclitaxel‐based chemotherapy for aggressive kaposiform hemangioendothelioma of the temporomastoid region: Case report and review of the literature
Authors: Funato Michinori , Fukao Toshiyuki , Sasai Hideo , Hori Tomohiro , Terazawa Daisuke , Kanda Kaori , Ozeki Michio , Mizuta Keisuke , Hirose Yoshinobu , Kaneko Hideo , Kondo Naomi 
Published: August 2012

AbstractBackgroundKaposiform hemangioendothelioma (KHE) is a rare vascular tumor of infancy and childhood. This tumor results in poor prognosis, and therefore, development of a more effective treatment is needed.Methods and ResultsWe describe an 11‐year‐old boy presenting with left facial palsy caused by aggressive KHE of the left temporomastoid region. He was treated with paclitaxel‐based chemotherapy, because of the difficulty with complete surgical resection for anatomic factor, multiple lung metastases on diagnosis, and no response to conventional treatments. This treatment reduced the volume of primary tumor and lung metastatic lesions, but the efficacy was transitory.ConclusionsPaclitaxel‐based chemotherapy for aggressive KHE may be effective, therefore the multimodality therapy including paclitaxel of aggressive KHE, particularly in the head and neck, needs to be investigated in further studies. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Aggressive multimodality management of locally advanced retromolar trigone tumors
Authors: Suryanarayana Deo S. V. , Shukla Nootan K. , Kallianpur Ashwin A. , Mohanti Bidhu K. , Thulkar Sanjay P. 
Published: August 2012

AbstractBackgroundRetromolar trigone tumors are rare and aggressive malignancies. There is lack of quality evidence pertaining to their management due to the heterogeneity in treatment policies adopted. We retrospectively reviewed the patients of locally advanced retromolar trigone tumors treated with a standard and uniform multimodality management.MethodsA retrospective review of patients with locally advanced retromolar trigone tumors was performed and an analysis of clinicopathologic profile, treatment details, and survival outcomes was carried out.ResultsForty‐two patients of locally advanced retromolar trigone tumors underwent the standard multimodality treatment. The majority of them presented with stage IVa disease. Margin negative resection could be achieved in 93% of patients. Histopathologically proven bone and node involvement was seen in 20 patients (47.6%) and 21 patients (50%), respectively. The 3‐year disease‐free and overall survival rates were 64% and 71%, respectively.ConclusionsTreatment of patients with locally advanced retromolar trigone tumors is challenging. However, good oncologic outcomes can be achieved by advocating an aggressive surgical approach with postoperative radiation therapy. © 2012 Wiley Periodicals, Inc. Head Neck, 2013
Global sensitivity analyses for a complex hydrological model applied in an Alpine watershed
Authors: Dobler C. , Pappenberger F. 
Published: August 2012

AbstractThe increasing complexity of hydrological models results in a large number of parameters to be estimated. In order to better understand how these complex models work, efficient screening methods are required in order to identify the most important parameters. This is of particular importance for models that are used within an operational real‐time forecasting chain such as HQsim. The objectives of this investigation are to (i) identify the most sensitive parameters of the complex HQsim model applied in the Alpine Lech catchment and (ii) compare model parameter sensitivity rankings attained from three global sensitivity analysis techniques. The techniques presented are the (i) regional sensitivity analysis, (ii) Morris analysis and (iii) state‐dependent parameter modelling. The results indicate that parameters affecting snow melt as well as processes in the unsaturated soil zone reveal high significance in the analysed catchment. The snow melt parameters show clear temporal patterns in the sensitivity whereas most of the parameters affecting processes in the unsaturated soil zone do not vary in importance across the year. Overall, the maximum degree day factor (meltfunc_max) has been identified to play a key role within the HQsim model. Although the parameter sensitivity rankings are equivalent between methods for a number of parameters, for several key parameters differing results were obtained. An uncertainty analysis demonstrates that a parameter ranking attained from only one method is subjected to large uncertainty. Copyright © 2012 John Wiley & Sons, Ltd.
Contribution of Na+,HCO3−‐cotransport to cellular pH control in human breast cancer: A role for the breast cancer susceptibility locus NBCn1 (SLC4A7)
Authors: Boedtkjer Ebbe , Moreira José M.A. , Mele Marco , Vahl Pernille , Wielenga Vera T. , Christiansen Peer M. , Jensen Vibeke E.D. , Pedersen Stine F. , Aalkjaer Christian 
Published: August 2012

AbstractGenome‐wide association studies recently linked the locus for Na+,HCO3−‐cotransporter NBCn1 (SLC4A7) to breast cancer susceptibility, yet functional insights have been lacking. To determine whether NBCn1, by transporting HCO3− into cells, may dispose of acid produced during high metabolic activity, we studied the expression of NBCn1 and the functional impact of Na+,HCO3−‐cotransport in human breast cancer. We found that the plasmalemmal density of NBCn1 was 20–30% higher in primary breast carcinomas and metastases compared to matched normal breast tissue. The increase in NBCn1 density was similar in magnitude to that observed for Na+/H+‐exchanger NHE1 (SLC9A1), a transporter previously implicated in cell migration, proliferation and malignancy. In primary breast carcinomas, the apparent molecular weight for NBCn1 was increased compared to normal tissue. Using pH‐sensitive fluorophores, we showed that Na+,HCO3−‐cotransport is the predominant mechanism of acid extrusion and is inhibited 34 ± 9% by 200 μM 4,4′‐diisothiocyanatostilbene‐2,2′‐disulfonic acid in human primary breast carcinomas. At intracellular pH (pHi) levels >6.6, CO2/HCO3−‐dependent mechanisms accounted for >90% of total net acid extrusion. Na+/H+‐exchange activity was prominent only at lower pHi‐values. Furthermore, steady‐state pHi was 0.35 ± 0.06 units lower in the absence than in the presence of CO2/HCO3−. In conclusion, expression of NBCn1 is upregulated in human primary breast carcinomas and metastases compared to normal breast tissue. Na+,HCO3−‐cotransport is a major determinant of pHi in breast cancer and the modest DIDS‐sensitivity is consistent with NBCn1 being predominantly responsible. Hence, our results suggest a major pathophysiological role for NBCn1 that may be clinically relevant.
Tumor‐initiating properties of breast cancer and melanoma cells in vivo are not invariably reflected by spheroid formation in vitro, but can be increased by long‐term culturing as adherent monolayers
Authors: Kuch Vanessa , Schreiber Caroline , Thiele Wilko , Umansky Viktor , Sleeman Jonathan P. 
Published: August 2012

AbstractCancer stem cells (CSCs) have been studied intensively in recent years due to their potential importance for understanding neoplastic disease and the design of antitumor therapies. A number of properties attributed to CSCs have been used to define the CSC population, the most important of which is the ability to initiate reproducibly the growth of tumors in vivo. Other assays such as spheroid formation, expression of particular markers and label retention are also used for defining CSCs, although the degree to which these assays invariably reflect the ability to form tumors in vivo remains to be carefully evaluated. Given the importance of correctly defining and isolating CSCs if valid conclusions about their characteristics are to be made, we used syngeneic animal models to compare these different assays. In standard spheroid assays, cell aggregation rather than spheroid growth from single cell suspensions ensued, but aggregation was circumvented by the inclusion of methylcellulose in the medium. Label‐retaining subpopulations did not reliably exhibit an enhanced ability to form spheroids and were enriched for senescent cells. Spheroid‐forming ability was found to correspond to expression of established CSC markers, although not invariably. Furthermore, spheroid‐forming ability was not always reflected in tumor‐initiating properties in vivo. Long‐term culture of primary mammary tumor cells as adherent monolayers increased their tumor‐initiating ability in vivo. This increase was attenuated when the cells were subsequently cultivated as spheroids. Together these data indicate that assays that are widely used to define CSC subpopulations do not invariably reflect tumor‐initiating properties in vivo.
High‐risk HPV testing on self‐sampled versus clinician‐collected specimens: A review on the clinical accuracy and impact on population attendance in cervical cancer screening
Authors: Snijders Peter J.F. , Verhoef Viola M.J. , Arbyn Marc , Ogilvie Gina , Minozzi Silvia , Banzi Rita , van Kemenade Folkert J. , Heideman Daniëlle A.M. , Meijer Chris J.L.M. 
Published: August 2012

AbstractThis review elaborates on the accuracy and feasibility of human papillomavirus (HPV) self‐sampling, i.e., offering self‐sampling of (cervico‐)vaginal cell material by women themselves in nonclinical settings for high‐risk HPV (hrHPV) detection in the laboratory, for cervical screening. To that end a bibliographic database search (PubMed) was performed to identify studies (published between January 1992 and January 2012) that compared clinical accuracy of HPV testing on self‐sampled material with that of cytology or HPV testing on clinician‐taken samples, and studies comparing response to offering HPV self‐sampling with a recall invitation. Overall, hrHPV testing on self‐samples appeared to be at least as, if not more, sensitive for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) as cytology on clinician‐obtained cervical samples, though often less specific. In most studies, hrHPV testing on self‐ and clinician‐sampled specimens is similarly accurate with respect to CIN2+ detection. Variations in clinical performance likely reflect the use of different combinations of collection devices and HPV tests. Because it is known that underscreened women are at increased risk of cervical cancer, targeting non‐attendees of the screening program could improve the effectiveness of cervical screening. In developed countries offering self‐sampling has shown to be superior to a recall invitation for cytology in re‐attracting original non‐attendees into the screening program. Additionally, self‐testing has shown to facilitate access to cervical screening for women in low resource areas. This updated review of the literature suggests that HPV self‐sampling could be an additional strategy that can improve screening performance compared to current cytology‐based call‐recall programs.
Synthesis and Development of Lipoprotein‐Based Nanocarriers for Light‐Activated Theranostics
Authors: Jin Honglin , Chen Juan , Lovell Jonathan F. , Zhang Zhihong , Zheng Gang 
Published: August 2012

AbstractThe design and synthesis of new light‐activated contrast agents for theranostics (therapy/diagnosis) has the potential to facilitate multifunctional and improved personalized medicine. The use of light as a remote activation strategy provides spatial and temporal control of drug effect and nanotechnology can play a key role in this process. Lipoproteins (LDL and HDL), which transport water‐insoluble cholesteryl esters and triacylglycerols in nature, have evolved to efficiently ferry exogenous hydrophobic compounds in vivo. They are naturally biocompatible, maneuverable due to their small size (<30 nm), and can be loaded through various methods, and are therefore ideal vehicles to load and transport hydrophobic theranostic agents. This review examines the history and ongoing research activities regarding the design and synthesis of lipoprotein‐based formulations, and their applications or potential applications as light‐activated theranostic agents, with a main focus on photodynamic therapy. This field, while still in its infancy, will benefit from improved design and modulation of enhanced lipoprotein‐based nanocarriers, with the ultimate goal of simultaneous imaging and photoactivation of therapeutic agents in a clinical setting.