bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dedicated microarray for in-depth analysis of pre-mRNA splicing events: application to the study of genes involved in the response to targeted anticancer therapies
Authors: Pesson Marine , Eymin Béatrice , De La Grange Pierre , Simon Brigitte , Corcos Laurent 
Published: January 2014

AbstractAlternative pre-mRNA splicing (AS) widely expands proteome diversity through the combinatorial assembly of exons. The analysis of AS on a large scale, by using splice-sensitive microarrays, is a highly efficient method to detect the majority of known and predicted alternative transcripts for a given gene. The response to targeted anticancer therapies cannot easily be anticipated without prior knowledge of the expression, by the tumor, of target proteins or genes. To analyze, in depth, transcript structure and levels for genes involved in these responses, includingAKT1-3,HER1-4,HIF1A,PIK3CA,PIK3R1-2,VEGFA-DandPIR, we engineered a dedicated gene chip with coverage of an average 185 probes per gene and, especially, exon-exon junction probes. As a proof of concept, we demonstrated the ability of such a chip to detect the effects of over-expressed SRSF2 RNA binding protein on the structure and abundance of mRNA products in H358 lung cancer cells conditionally over-expressing SRSF2. Major splicing changes were observed, including inHER1/EGFRpre-mRNA, which were also seen in human lung cancer samples over-expressing the SRSF2 protein. In addition, we showed that variations inHER1/EGFRpre-mRNA splicing triggered by SRSF2 overexpression in H358 cells resulted in a drop in HER1/EGFR protein level, which correlated with increased sensitivity to gefitinib, an EGFR tyrosine kinase inhibitor. We propose, therefore, that this novel tool could be especially relevant for clinical applications, with the aim to predict the response before treatment.
Efficacy of interventions that include diet, aerobic and resistance training components for type 2 diabetes prevention: a systematic review with meta-analysis
Authors: Aguiar Elroy J , Morgan Philip J , Collins Clare E , Plotnikoff Ronald C , Callister Robin 
Published: January 2014

Abstract
Current recommendations for the prevention of type 2 diabetes advise modification of diet and exercise behaviors including both aerobic and resistance training. However, the efficacy of multi-component interventions involving a combination of these three components has not been established. The aims of this review were to systematically review and meta-analyze the evidence on multi-component (diet + aerobic exercise + resistance training) lifestyle interventions for type 2 diabetes prevention. Eight electronic databases (Medline, Embase, SportDiscus, Web of Science, CINAHL, Informit health collection, Cochrane library and Scopus) were searched up to June 2013. Eligible studies 1) recruited prediabetic adults or individuals at risk of type 2 diabetes; 2) conducted diet and exercise [including both physical activity/aerobic and resistance training] programs; and 3) reported weight and plasma glucose outcomes. In total, 23 articles from eight studies were eligible including five randomized controlled trials, one quasi-experimental, one two-group comparison and one single-group pre-post study. Four studies had a low risk of bias (score ≥ 6/10). Median intervention length was 12 months (range 4–48 months) with a follow-up of 18 months (range 6.5 - 48 months). The diet and exercise interventions varied slightly in terms of their specific prescriptions. Meta-analysis favored interventions over controls for weight loss (-3.79 kg [-6.13, -1.46; 95% CI], Z = 3.19, P = 0.001) and fasting plasma glucose (-0.13 mmol.L-1 [-0.24, -0.02; 95% CI], Z = 2.42, P = 0.02). Diabetes incidence was only reported in two studies, with reductions of 58% and 56% versus control groups. In summary, multi-component lifestyle type 2 diabetes prevention interventions that include diet and both aerobic and resistance exercise training are modestly effective in inducing weight loss and improving impaired fasting glucose, glucose tolerance, dietary and exercise outcomes in at risk and prediabetic adult populations. These results support the current exercise guidelines for the inclusion of resistance training in type 2 diabetes prevention, however there remains a need for more rigorous studies, with long-term follow-up evaluating program efficacy, muscular fitness outcomes, diabetes incidence and risk reduction.
Extended photoresponse and multi-band luminescence of ZnO/ZnSe core/shell nanorods
Authors: Yang Qin , Cai Hua , Hu Zhigao , Duan Zhihua , Yang Xu , Sun Jian , Xu Ning , Wu Jiada 
Published: January 2014

Abstract
Aligned ZnO/ZnSe core/shell nanorods (NRs) with type-II energy band alignment were fabricated by pulsed laser deposition of ZnSe on the surfaces of hydrothermally grown ZnO NRs. The obtained ZnO/ZnSe core/shell NRs are composed of wurtzite ZnO cores and zinc blende ZnSe shells. The bare ZnO NRs are capable of emitting strong ultraviolet (UV) near band edge (NBE) emission at 325-nm light excitation, while the ZnSe shells greatly suppress the emission from the ZnO cores. High-temperature processing results in an improvement in the structures of the ZnO cores and the ZnSe shells and significant changes in the optical properties of ZnO/ZnSe core/shell NRs. The fabricated ZnO/ZnSe core/shell NRs show optical properties corresponding to the two excitonic band gaps of wurtzite ZnO and zinc blende ZnSe and the effective band gap between the conduction band minimum of ZnO and the valence band maximum ZnSe. An extended photoresponse much wider than those of the constituting ZnO and ZnSe and a multi-band photoluminescence including the UV NBE emission of ZnO and the blue NBE emission of ZnSe are observed.
Enhanced state selection Markov model for image splicing detection
Authors: Su Bo , Yuan Quanqiao , Wang Shilin , Zhao Chenglin , Li Shenghong 
Published: January 2014

AbstractDigital image splicing blind detection is becoming a new and important subject in information security area. Among various approaches in extracting splicing clues, Markov state transition probability feature based on transform domain (discrete cosine transform or discrete wavelet transform) seems to be most promising in the state of the arts. However, the up-to-date extraction method of Markov features has some disadvantages in not exploiting the information of transformed coefficients thoroughly. In this paper, an enhanced approach of Markov state selection is proposed, which matches coefficients to Markov states base on well-performed function model. Experiments and analysis show that the improved Markov model can employ more useful underlying information in transformed coefficients and can achieve a higher recognition rate as results.
Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters
Authors: Chiang Austin WT , Liu Wei-Chung , Charusanti Pep , Hwang Ming-Jing 
Published: January 2014

Abstract

Background
A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system’s dynamics.

Results
We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics.

Conclusions
A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.
Comparison of healing rate in diabetes‐related foot ulcers with low frequency ultrasonic debridement versus non‐surgical sharps debridement: a randomised trial protocol
Authors: Michailidis Lucia , Williams Cylie M , Bergin Shan M , Haines Terry P 
Published: January 2014

AbstractBackgroundFoot ulceration has been reported as the leading cause of hospital admission and amputation in individuals with diabetes. Diabetes‐related foot ulcers require multidisciplinary management and best practice care, including debridement, offloading, dressings, management of infection, modified footwear and management of extrinsic factors.Ulcer debridement is a commonly applied management approach involving removal of non‐viable tissue from the ulcer bed. Different methods of debridement have been reported in the literature including autolytic debridement via moist wound healing, mechanical debridement utilising wet to dry dressings, theatre based sharps debridement, biological debridement, non‐surgical sharps debridement and newer technology such as low frequency ultrasonic debridement.MethodsPeople with diabetes and a foot ulcer, referred to and treated by the Podiatry Department at Monash Health and who meet the inclusion criteria will be invited to participate in this randomised controlled trial. Participants will be randomly and equally allocated to either the non‐surgical sharps debridement (control) or low frequency ultrasonic debridement (intervention) group (n = 322 ulcers/n = 108 participants).Where participants have more than one ulcer, only the participant will be randomised, not the ulcer. An investigator not involved in participant recruitment or assessment will be responsible for preparing the random allocation sequence and envelopes.Each participant will receive weekly treatment for six months including best practice podiatric management. Each ulcer will be measured on a weekly basis by calculating total area in centimetres squared. Measurement will be undertaken by a trained research assistant to ensure outcomes are blinded from the treating podiatrist. Another member of the research team will assess the final primary outcome.DiscussionThe primary aim of this study is to compare healing rates for diabetes‐related foot ulcers using non‐surgical sharps debridement versus low frequency ultrasonic debridement over a six month period. The primary outcome measure for this study is the proportion of ulcers healed by the six month follow‐up period.Secondary outcomes will include a quality of life measure, assessment of pain and health care resource use between the two treatment modalities.Trial registrationAustralian New Zealand Clinical Trial Registry: ACTRN12612000490875.
Human cadaver multipotent stromal/stem cells isolated from arteries stored in liquid nitrogen for 5 years
Authors: Valente Sabrina , Alviano Francesco , Ciavarella Carmen , Buzzi Marina , Ricci Francesca , Tazzari Pier Luigi , Pagliaro Pasqualepaolo , Pasquinelli Gianandrea 
Published: January 2014

Abstract
Introduction
Regenerative medicine challenges researchers to find noncontroversial, safe and abundant stem cell sources. In this context, harvesting from asystolic donors could represent an innovative and unlimited reservoir of different stem cells. In this study, cadaveric vascular tissues were established as an alternative source of human cadaver mesenchymal stromal/stem cells (hC-MSCs). We reported the successful cell isolation from postmortem arterial segments stored in a tissue-banking facility for at least 5 years.

Methods
After thawing, hC-MSCs were isolated with a high efficiency (12 × 106) and characterized with flow cytometry, immunofluorescence, molecular and ultrastructural approaches.

Results
In early passages, hC-MSCs were clonogenic, highly proliferative and expressed mesenchymal (CD44, CD73, CD90, CD105, HLA-G), stemness (Stro-1, Oct-4, Notch-1), pericyte (CD146, PDGFR-β, NG2) and neuronal (Nestin) markers; hematopoietic and vascular markers were negative. These cells had colony and spheroid-forming abilities, multipotency for their potential to differentiate in multiple mesengenic lineages and immunosuppressive activity to counteract proliferation of phytohemagglutinin-stimulated blood mononuclear cells.

Conclusions
The efficient procurement of stem cells from cadaveric sources, as postmortem vascular tissues, demonstrates that such cells can survive to prolonged ischemic insult, anoxia, freezing and dehydration injuries, thus paving the way for a scientific revolution where cadaver stromal/stem cells could effectively treat patients demanding cell therapies.
Normal functions and the height of Gross-Schoen cycles
Authors: Jong Robin De 
Published: January 2014

AbstractWe prove a variant of a formula due to Zhang relating the Beilinson– Bloch height of the Gross–Schoen cycle on a pointed curve with the self-intersection of its relative dualizing sheaf. In our approach, the height of the Gross–Schoen cycle occurs as the degree of a suitable Bloch line bundle. We show that the Chern form of this line bundle is nonnegative, and we calculate its class in the Picard group of the moduli space of pointed stable curves of compact type. The basic tools are normal functions and biextensions associated to the cohomology of the universal Jacobian.
Early motor deficits in mouse disease models are reliably uncovered using an automated home cage wheel-running system: a cross-laboratory validation
Authors: Mandillo Silvia , Heise Ines , Garbugino Luciana , Tocchini-Valentini Glauco P. , Giuliani Alessandro , Wells Sara , Nolan Patrick M. 
Published: January 2014

Summary
Deficits in motor function are debilitating features in disorders affecting neurological, neuromuscular and musculoskeletal systems. Although these can vary greatly with respect to age of onset, symptomatic presentation, rate of progression and severity, the study of these disease models in mice is confined to use of a small number of tests, most commonly the Rotarod test. To expand the repertoire of meaningful motor function tests in mice, we tested, optimised and validated an automated home-cage based running-wheel system, incorporating a conventional wheel with evenly-spaced rungs and a complex wheel with particular rungs absent. The system enables automated assessment of motor function without handler interference which is desirable in longitudinal studies involving continuous monitoring of motor performance. In baseline studies at two test centres, consistently significant differences in performance on both wheels were detectable among four common inbred strains. As further validation, we studied performance in mutant models of progressive neurodegenerative disease, Huntington's Disease, TgN(HD82Gln)81Dbo (HD) and Amyotrophic Lateral Sclerosis, Tg(SOD1G93A)dl1/GurJ (SOD1) and in a mutant strain with subtle gait abnormalities, C-Snap25Bdr/H (Blind-drunk, Bdr). In both models of progressive disease, as with the third mutant, we could reliably and consistently detect specific motor function deficits at ages far earlier than any previously-recorded symptoms in vivo, 7-8 weeks for the HD mice and 12 weeks for the SOD1 mice. This included longitudinal analysis of Rotarod and grip strength performance where deficits were still not detectable at 12 weeks and 23 weeks respectively. Several new parameters of motor behaviour were uncovered using Principal Component Analysis, indicating that the wheel-running assay could record features of motor function that are independent of Rotarod performance. This represents a powerful new method to detect motor deficits at pre-symptomatic stages in mouse disease models and should be considered as a valid tool to investigate the efficacy of therapeutic agents.
Sodium Hypochlorite-promoted Novel Synthesis of Organic Ammonium Tribromides and Application of Phenanthroline Hydrotribromide in Chemoselective Oxidation of Organic Sulfides by Hydrogen Peroxide
Authors: Dey Madhudeepa , Dey Rupa R , Dhar Siddhartha S 
Published: January 2014

Abstract
A novel method of synthesis of organic ammonium tribromides (OATBs) is developed by using an inexpensive and eco-friendly sodium hypochlorite as oxidant for conversion of Br− to Br3−. The OATBs thus prepared include both quaternary ammonium tribromides and N-heterocyclic tribromides. A new addition to the family of OATBs is made in the form of phenanthroline hydrotribromide. The efficacy of this new tribromide as catalyst is ascertained in the oxidative transformation of organic sulfides to their corresponding sulfoxides and sulfones by hydrogen peroxide.
Observation of a unique case of metastatic basal cell carcinoma found by radiographic evaluation in a patient with oculocutaneous albinism
Authors: Johnston Mickaila , Winham Whitney , Massoll Nicole , Gardner Jerad M. 
Published: January 2014

Background:Basal cell carcinoma is one of the more common cancers worldwide; 2.8 million are diagnosed annually in the USA. However, the rate at which it metastasizes is considered very low, between 0.0028 and 0.5%. For those rare cases in which metastases occur, approximately one third metastasize to the lung. Case:Presented is a 62-year-old Caucasian male with oculocutaneous albinism and a history of basal cell carcinomas occurring in multiple anatomic sites, most recently at the bilateral forearm and back. Surveillance PET/CT imaging led to the discovery of no less than 30 lung nodules which were consistent with basal cell carcinoma on biopsy. Histological features were remarkably similar in both the primary tumor and in the metastases.Conclusion: An unusual case of a non-head and neck primary basal cell carcinoma metastatic to the lung was discovered on surveillance PET/CT imaging, in a patient with oculocutaneous albinism.
Typification of names and taxonomic notes within the genus Thymus L. (Lamiaceae)
Authors: Bartolucci Fabrizio , Peruzzi Lorenzo , Passalacqua Nicodemo 
Published: January 2014

AbstractThymus is one of the most critical genera of the Euro–Mediterranean flora and most of its taxa are in need of typification. During a preliminary study on the taxonomy of this genus in the Mediterranean area, several names turned out to be not yet typified. In order to fix their applications, nomenclatural types for 18 names within the genus Thymus are here designated. The new combination Thymus praecox subsp. parvulus (Lojac.) Bartolucci, Peruzzi & N.G. Passal. is also proposed.
Revised taxonomy and nomenclature of Acalypha sect. Communes (Euphorbiaceae), a complex group of species widespread in the north of the Southern Cone
Authors: Cardiel José María , Rodríguez Pablo Muñoz , Garmendia Félix Muñoz 
Published: January 2014

AbstractThe application of the species names included in the previously invalidly published “Acalypha sect. Communes”, mostly around the widely cited A. communis, has been confusing almost since their publication. After a thorough study of the literature, from which we recorded 56 scientific names associated to this section, as well as the study of ca. 1500 herbarium specimens, including nomenclatural types, we propose a deep nomenclatural and taxonomic reorganization of this group. Acalypha sect. Communes is validly published and circumscribed to include five species: Acalypha communis, A. variabilis, A. vellamea, A. senilis and A. hassleriana. Regarding A. communis, we delimit its taxonomic status and propose five subspecies: A. communis subsp. communis, subsp. apicalis, subsp. paraguariensis, subsp. saltensis and subsp. tracheliifolia, four of them new combinations. Twenty–two lectotypes and three neotypes are designated, and 20 new synonyms are proposed. A key based on morphological characters to the species and subspecies of this section is also provided.
A molecular phylogeny and classification of the largely succulent and mainly African Euphorbia subg. Athymalus (Euphorbiaceae)
Authors: Peirson Jess A. , Bruyns Peter V. , Riina Ricarda , Morawetz Jeffery J. , Berry Paul E. 
Published: January 2014

AbstractEuphorbia subg. Athymalus consists of approximately 150 species and is one of the four main lineages that comprise the species–rich genus Euphorbia. Most species in the subgenus are stem succulents with greatly reduced leaves, but there are also leafy herbs, shrubs, trees and geophytes. The subgenus is restricted to arid regions of the Old World. Most species are found in sub–Saharan Africa, with one in Macaronesia and adjacent parts of western Africa, a few in the Arabian Peninsula (one of which extends into Iran) and one native to Madagascar. Twenty–three species are endemic to the northeastern Horn of Africa (SE Ethiopia, Socotra, Somalia), while 72 species are restricted to southern Africa (including Botswana, Lesotho, Namibia, South Africa and Swaziland). Sixty of those are endemic to South Africa alone, where they are particularly associated with the semi–arid west and south of the country in the Greater Cape Floristic Region and the Nama Karoo Region. We sampled 88 species and analyzed data from the nuclear ribosomal ITS and plastid ndhF regions. Analyses of the separate and combined datasets produced phylogenies that confirm the monophyly of E. subg. Athymalus and the placement of E. antso from Madagascar as sister to the rest of the subgenus. Our analyses also show that the subgenus consists of a grade of early–diverging lineages that are relatively poor in species and that the major radiation of succulent species in southern Africa forms a highly supported clade (E. sect. Anthacanthae). Species–level relationships within this southern African clade, however, remain largely unresolved. Our phylogenetic hypotheses allow us to propose a new classification for E. subg. Athymalus where seven sections are recognized, two of which are newly described. The large southern African E. sect. Anthacanthae is further divided into five subsections, and four series are recognized in E. subsect. Florispinae.
The fern genus Adenoderris (family incertae sedis) is artificial
Authors: McHenry Monique A. , Sundue Michael A. , Barrington David S. 
Published: January 2014

AbstractFor over a century the relationships of the rare fern genus Adenoderris J. Sm. have been confused. Here, we (1) present a molecular analysis of the genus based on multiple chloroplast markers with the goal of placing its species phylogenetically, (2) provide insights into its morphology and complex taxonomy, and (3) make relevant nomenclatural changes. In seeking a resolution of the problems with Adenoderris, we investigated the morphological, historical, ecological, and biogeographical factors that have made Adenoderris so difficult to place with certainty. The key findings are that (1) Adenoderris comprises two species that were included in the genus on the basis of convergent and symplesiomorphic morphological features, and (2) though the two species both lie in the Dryopteridaceae, they belong to different genera. The correct names for these two species are Polystichum glandulosum C. Presl and Dryopteris sororia (Maxon) M. McHenry, Sundue & Barrington, comb. nov.