bluuebunny/crossref_metadata_2025_split huggingface dataset:
Split Bregman multicoil accelerated reconstruction technique: A new framework for rapid reconstruction of cardiac perfusion MRI
Authors: Kamesh Iyer Srikant , Tasdizen Tolga , Likhite Devavrat , DiBella Edward 
Published: March 2016

Purpose:Rapid reconstruction of undersampled multicoil MRI data with iterative constrained reconstruction method is a challenge. The authors sought to develop a new substitution based variable splitting algorithm for faster reconstruction of multicoil cardiac perfusion MRI data.Methods:The new method, split Bregman multicoil accelerated reconstruction technique (SMART), uses a combination of split Bregman based variable splitting and iterative reweighting techniques to achieve fast convergence. Total variation constraints are used along the spatial and temporal dimensions. The method is tested on nine ECG‐gated dog perfusion datasets, acquired with a 30‐ray golden ratio radial sampling pattern and ten ungated human perfusion datasets, acquired with a 24‐ray golden ratio radial sampling pattern. Image quality and reconstruction speed are evaluated and compared to a gradient descent (GD) implementation and to multicoil k‐t SLR, a reconstruction technique that uses a combination of sparsity and low rank constraints.Results:Comparisons based on blur metric and visual inspection showed that SMART images had lower blur and better texture as compared to the GD implementation. On average, the GD based images had an ∼18% higher blur metric as compared to SMART images. Reconstruction of dynamic contrast enhanced (DCE) cardiac perfusion images using the SMART method was ∼6 times faster than standard gradient descent methods. k‐t SLR and SMART produced images with comparable image quality, though SMART was ∼6.8 times faster than k‐t SLR.Conclusions:The SMART method is a promising approach to reconstruct good quality multicoil images from undersampled DCE cardiac perfusion data rapidly.
The Human Papillomavirus 16 E7 Oncoprotein Attenuates AKT Signaling To Promote Internal Ribosome Entry Site-Dependent Translation and Expression of c-MYC
Authors: Strickland Sydney Webb , Vande Pol Scott 
Published: March 2016

ABSTRACTWhile the role of high-risk human papillomavirus (HPV) oncoproteins E6 and E7 in targeting p53 and retinoblastoma (Rb) has been intensively studied, how E6 and E7 manipulate cellular signaling cascades to promote the viral life cycle and cancer development is less understood. Keratinocytes containing the episomal HPV-16 genome had decreased activation of AKT, which was phenocopied by HPV-16 E7 expression alone. Attenuation of phosphorylated AKT (pAKT) by E7 was independent of the Rb degradation function of E7 but could be ablated by a missense mutation in the E7 carboxy terminus, H73E, thereby defining a novel structure-function phenotype for E7. Downstream of AKT, reduced phosphorylation of p70 S6K and 4E-BP1 was also observed in E7-expressing keratinocytes, which coincided with an increase in internal ribosomal entry site (IRES)-dependent translation that enhanced the expression of several cellular proteins, including MYC, Bax, and the insulin receptor. The decrease in pAKT mediated by E7 is in contrast to the widely observed increase of pAKT in invasive cervical cancers, suggesting that the activation of AKT signaling could be acquired during the progression from initial productive infections to invasive carcinomas.IMPORTANCEHPV causes invasive cervical cancers through the dysregulation of the cell cycle regulators p53 and Rb, which are degraded by the viral oncoproteins E6 and E7, respectively. Signaling cascades contribute to cancer progression and cellular differentiation, and how E6 and E7 manipulate those pathways remains unclear. The phosphoinositol 3-kinase (PI3K)/AKT pathway regulates cellular processes, including proliferation, cell survival, and cell differentiation. Surprisingly, we found that HPV-16 decreased the phosphorylation of AKT (pAKT) and that this is a function of E7 that is independent of the Rb degradation function. This is in contrast to the observed increase in AKT signaling in nearly 80% of cervical cancers, which typically show an acquired mutation within the PI3K/AKT cascade leading to constitutive activation of the pathway. Our observations suggest that multiple changes in the activation and effects of AKT signaling occur in the progression from productive HPV infections to invasive cervical cancers.
Global Genomic Diversity of Human Papillomavirus 11 Based on 433 Isolates and 78 Complete Genome Sequences
Authors: Jelen Mateja M. , Chen Zigui , Kocjan Boštjan J. , Hošnjak Lea , Burt Felicity J. , Chan Paul K. S. , Chouhy Diego , Combrinck Catharina E. , Estrade Christine , Fiander Alison , Garland Suzanne M. , Giri Adriana A. , González Joaquín Víctor , Gröning Arndt , Hibbitts Sam , Luk Tommy N. M. , Marinic Karina , Matsukura Toshihiko , Neumann Anna , Oštrbenk Anja , Picconi Maria Alejandra , Sagadin Martin , Sahli Roland , Seedat Riaz Y. , Seme Katja , Severini Alberto , Sinchi Jessica L. , Smahelova Jana , Tabrizi Sepehr N. , Tachezy Ruth , Tohme Faybush Sarah , Uloza Virgilijus , Uloziene Ingrida , Wong Yong Wee , Židovec Lepej Snježana , Burk Robert D. , Poljak Mario 
Published: March 2016

ABSTRACT

Human papillomavirus 11
(HPV11) is an etiological agent of anogenital warts and laryngeal papillomas and is included in the 4-valent and 9-valent prophylactic HPV vaccines. We established the largest collection of globally circulating HPV11 isolates to date and examined the genomic diversity of 433 isolates and 78 complete genomes (CGs) from six continents. The genomic variation within the 2,800-bp E5a-E5b-L1-upstream regulatory region was initially studied in 181/207 (87.4%) HPV11 isolates collected for this study. Of these, the CGs of 30 HPV11 variants containing unique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes were fully sequenced. A maximum likelihood tree based on the global alignment of 78 HPV11 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (lineages A and B) and four sublineages (sublineages A1, A2, A3, and A4). HPV11 (sub)lineage-specific SNPs within the CG were identified, as well as the 208-bp representative region for CG-based phylogenetic clustering within the partial E2 open reading frame and noncoding region 2. Globally, sublineage A2 was the most prevalent, followed by sublineages A1, A3, and A4 and lineage B.

IMPORTANCE
This collaborative international study defined the global heterogeneity of HPV11 and established the largest collection of globally circulating HPV11 genomic variants to date. Thirty novel complete HPV11 genomes were determined and submitted to the available sequence repositories. Global phylogenetic analysis revealed two HPV11 variant lineages and four sublineages. The HPV11 (sub)lineage-specific SNPs and the representative region identified within the partial genomic region E2/noncoding region 2 (NCR2) will enable the simpler identification and comparison of HPV11 variants worldwide. This study provides an important knowledge base for HPV11 for future studies in HPV epidemiology, evolution, pathogenicity, prevention, and molecular assay development.
B Cell Responses during Secondary Dengue Virus Infection Are Dominated by Highly Cross-Reactive, Memory-Derived Plasmablasts
Authors: Priyamvada Lalita , Cho Alice , Onlamoon Nattawat , Zheng Nai-Ying , Huang Min , Kovalenkov Yevgeniy , Chokephaibulkit Kulkanya , Angkasekwinai Nasikarn , Pattanapanyasat Kovit , Ahmed Rafi , Wilson Patrick C. , Wrammert Jens 
Published: March 2016

ABSTRACT
Dengue virus (DENV) infection results in the production of both type-specific and cross-neutralizing antibodies. While immunity to the infecting serotype is long-lived, heterotypic immunity wanes a few months after infection. Epidemiological studies link secondary heterotypic infections with more severe symptoms, and cross-reactive, poorly neutralizing antibodies have been implicated in this increased disease severity. To understand the cellular and functional properties of the acute dengue virus B cell response and its role in protection and immunopathology, we characterized the plasmablast response in four secondary DENV type 2 (DENV2) patients. Dengue plasmablasts had high degrees of somatic hypermutation, with a clear preference for replacement mutations. Clonal expansions were also present in each donor, strongly supporting a memory origin for these acutely induced cells. We generated 53 monoclonal antibodies (MAbs) from sorted patient plasmablasts and found that DENV-reactive MAbs were largely envelope specific and cross neutralizing. Many more MAbs neutralized DENV than reacted to envelope protein, emphasizing the significance of virion-dependent B cell epitopes and the limitations of envelope protein-based antibody screening. A majority of DENV-reactive MAbs, irrespective of neutralization potency, enhanced infection by antibody-dependent enhancement (ADE). Interestingly, even though DENV2 was the infecting serotype in all four patients, several MAbs from two patients neutralized DENV1 more potently than DENV2. Further, half of all type-specific neutralizing MAbs were also DENV1 biased in binding. Taken together, these findings are reminiscent of original antigenic sin (OAS), given that the patients had prior dengue virus exposures. These data describe the ongoing B cell response in secondary patients and may further our understanding of the impact of antibodies in dengue virus pathogenesis.

IMPORTANCE
In addition to their role in protection, antibody responses have been hypothesized to contribute to the pathology of dengue. Recent studies characterizing memory B cell (MBC)-derived MAbs have provided valuable insight into the targets and functions of B cell responses generated after DENV exposure. However, in the case of secondary infections, such MBC-based approaches fail to distinguish acutely induced cells from the preexisting MBC pool. Our characterization of plasmablasts and plasmablast-derived MAbs provides a focused analysis of B cell responses activated during ongoing infection. Additionally, our studies provide evidence of OAS in the acute-phase dengue virus immune response, providing a basis for future work examining the impact of OAS phenotype antibodies on protective immunity and disease severity in secondary infections.
Risk evaluation, detection and simulation during effusive eruption disasters
Authors: Harris Andrew , De Groeve Tom , Carn Simon , Garel Fanny 
Published: March 2016

Abstract
Lava ingress into a vulnerable population will be difficult to control, so that evacuation will be necessary for communities in the path of the active lava, followed by post-event population, infrastructural, societal and community replacement and/or relocation. There is a pressing need to set up a response chain that bridges scientists and responders during an effusive crisis to allow near-real-time delivery of globally standard ‘products’ for a timely and adequate humanitarian response. In this chain, the scientific research groups investigating lava remote-sensing and modelling need to provide products that are both useful to, and trusted by, the crisis response community. Requirements for these products include (a) formats that can be immediately integrated into a crisis management procedure, and (b) in an agreed and stable standard. A review of current capability reveals that we are at a point where the community can provide such a response, as is the aim of the RED SEED (Risk Evaluation, Detection and Simulation during Effusive Eruption Disasters) working group. This book is the first production of this group and is intended not only as a directory of current capabilities and operational service providers, but also as a statement of intent and need, while providing a simulation designed to demonstrate how a truly pan-disciplinary response to an effusive crisis could work.
Acute Fatty Liver of Pregnancy: A Review of Maternal Morbidity in 13 Patients Seen Over 12 Years in Nova Scotia
Authors: Hoare Connie D , Malatjalian Dickran A , Badley Bernard W , Sidorov Joseph J , Williams C Noel 
Published: March 2016

OBJECTIVE: To review the maternal and fetal survival in all cases of acute fatty liver of pregnancy seen by the Division of Gastroenterology at Grace Maternity Hospital and the Victoria General Hospital from 1979-91.DESIGN: A retrospective review of the clinical data obtained from the medical charts of 13 patients with a liver biopsy-based histopathological diagnosis of acute fatty liver of pregnancy.SETTING: Grace Maternity Hospital, a tertiary care centre serving d1e Atlantic provinces. Twelve patients were subsequently transferred to Victoria General Hospital for postpartum management in the setting of the medical intensive care unit.MAIN OUTCOME MEASURES: Classically, acute fatty liver of pregnancy is complicated by over 70% maternal and fetal mortality rate. Recent reports have indicated significantly improved maternal and fetal survival because of more awareness, improved management and the identification of milder forms of the disease.RESULTS: In this study of 13 cases of acute fatty liver of pregnancy, maternal survival was 100% and fetal survival was 93%.CONCLUSION: The excellent maternal and fetal survival in this series is attributed co awareness, close collaboration between obstetricians and gastroenterologists, prompt diagnosis and delivery and the management of postpartum patients in an intensive care unit setting.
A New Validation Approach of a New Three-Phase High Voltage Power Supply for Microwaves Generators with one Magnetron by Phase
Authors: Bassoui M. , Ferfra M. , Chraygane M. 
Published: March 2016

In order to validating the new three-phase High voltage power supply for microwave generators with one magnetron by phase, this paper presents a new validation approach to evaluate the proposed model with several evaluations. This approach is based on the calculation and measurement of the performance and the power factor of this new three-phase power supply, also the study of the operation of this new system in case of failure. The design of this power supply is composed of new three-phase transformer with magnetic shunt, supplying by phase a voltage doubler cell composed of a capacitor and a diode. Each cell in turn, supplies a single magnetron. In this paper we have presented the new three-phase transformer by its equivalent model; it’s a π quadruple model composed of storable inductances able to translating the nonlinear saturation phenomena for stabilization of the magnetron current. The voltage and current curves obtained by simulation with MATLAB SIMULINK are in good conformity with those obtained by experimental of conventional power supply using a single phase transformer for one magnetron.<strong> </strong>The same curves will allow us to plot the instantaneous power absorbed by each magnetron. This leads to determine the average power emitted by each magnetron, and establish the balance of the power microwave generator by computing its performance which is compared to that obtained from experimental. After that we will compute the power factor of this power supply and we will study its operation in case of failure of one or two magnetrons.
Novel ROADM modelling with WSS and OBS to Improve Routing Performance in Optical Network
Authors: G.R Kavitha , T.S Indumathi 
Published: March 2016

<span>The area of optical network is on constant point of focus among the research communities owing to potential advantage of long distance communication as well as the routing issues associated with it. Majority of the implemented techniques calls for using expensive hardware or adopting narrowed technical assumptions, for which reason the routing performance couldn’t be optimized to a large extent. The present manuscript proposes a novel technique called as Optimized Routing for Peak Traffic under the scenario of uncertainties in the existing traffic scenario. The proposed solution presents some potential principle that is incorporated in the ROADM design for enhancing the capabilities of the proposed system. The system is evaluated under multiple scenarios of analysis using blocking probabilities, OSNR, bit error rate, iteration etc. The outcome of the proposed system is compared with the one of the existing significant study to benchmark it.</span>
Experimental Investigations of the Self-Controlled Synchronous Motor Connected to a Three-Phase Line Commutated SCR Inverter
Authors: Chakraborty Tapan Kumar 
Published: March 2016

<p>This paper concerns the experimental investigations of the three-phase line commutated SCR inverter fed synchronous motor. The fabricated system consists of a line-commuted inverter, a three-phase synchronous motor with the excitation winding connected in series to the inverter input, a terminal voltage sensor and a gate-pulse generating circuit. The firing pulses for SCRs of the inverter are generated by the microprocessor in proper sequence with the help of synchronizing signal derived from the terminal voltages of the synchronous machine. The steady state performance characteristics are obtained experimentally using the fabricated system. The experimental results show that a three-phase synchronous motor supplied by a line commutated inverter with the excitation winding connected in series to the dc link provide excellent characteristics of the conventional dc series motor.</p><p> </p>
Performance and High Robustness DPC for PWM Rectifier under Unstable Direct Voltage Bus
Authors: Djebbar M.S. , Benalla H. 
Published: March 2016

This paper proposes a strategy de controlling a static AC/DC converter based on direct power control (DPC). The instantaneous active and reactive power is controlled in such a way to ensure the PWM rectifier with a sinusoidal current absorption. This control has proven effective in terms of reduction of total harmonic distortion (THD) of current absorbed. Offers a good control of active and reactive power with an operation at unitary power factor. The test of robustness carried out and the results have proven DPC good performance with strong possibility of de integrate it into the field of high voltage and high power as electric traction.
Genetic basis of PD-L1 overexpression in diffuse large B-cell lymphomas
Authors: Georgiou Konstantinos , Chen Longyun , Berglund Mattias , Ren Weicheng , de Miranda Noel F. C. C. , Lisboa Susana , Fangazio Marco , Zhu Shida , Hou Yong , Wu Kui , Fang Wenfeng , Wang Xianhuo , Meng Bin , Zhang Li , Zeng Yixin , Bhagat Govind , Nordenskjöld Magnus , Sundström Christer , Enblad Gunilla , Dalla-Favera Riccardo , Zhang Huilai , Teixeira Manuel R. , Pasqualucci Laura , Peng Roujun , Pan-Hammarström Qiang 
Published: March 2016

Key PointsTranslocations between PD-L1 and the IGH locus represent a genetic mechanism of PD-L1 overexpression in DLBCL. Genetic alterations in the PD-L1/PDL-2 locus are mainly associated with the non-GCB subtype of DLBCL.
Do little interactions get lost in dark random forests?
Authors: Wright Marvin N. , Ziegler Andreas , König Inke R. 
Published: March 2016

Abstract
Background
Random forests have often been claimed to uncover interaction effects. However, if and how interaction effects can be differentiated from marginal effects remains unclear. In extensive simulation studies, we investigate whether random forest variable importance measures capture or detect gene-gene interactions. With capturing interactions, we define the ability to identify a variable that acts through an interaction with another one, while detection is the ability to identify an interaction effect as such.

Results
Of the single importance measures, the Gini importance captured interaction effects in most of the simulated scenarios, however, they were masked by marginal effects in other variables. With the permutation importance, the proportion of captured interactions was lower in all cases. Pairwise importance measures performed about equal, with a slight advantage for the joint variable importance method. However, the overall fraction of detected interactions was low. In almost all scenarios the detection fraction in a model with only marginal effects was larger than in a model with an interaction effect only.

Conclusions
Random forests are generally capable of capturing gene-gene interactions, but current variable importance measures are unable to detect them as interactions. In most of the cases, interactions are masked by marginal effects and interactions cannot be differentiated from marginal effects. Consequently, caution is warranted when claiming that random forests uncover interactions.
The microenvironment controls invadosome plasticity
Authors: Di Martino Julie , Henriet Elodie , Ezzoukhry Zakaria , Goetz Jacky G. , Moreau Violaine , Saltel Frederic 
Published: March 2016

ABSTRACT
Invadosomes are actin-based structures involved in extracellular matrix degradation. Invadosomes is a term that includes podosomes and invadopodia, which decorate normal and tumour cells, respectively. They are mainly organised into dots or rosettes, and podosomes and invadopodia are often compared and contrasted. Various internal or external stimuli have been shown to induce their formation and/or activity. In this Commentary, we address the impact of the microenvironment and the role of matrix receptors on the formation, and dynamic and degradative activities of invadosomes. In particular, we highlight recent findings regarding the role of type I collagen fibrils in inducing the formation of a new linear organisation of invadosomes. We will also discuss invadosome plasticity more generally and emphasise its physio-pathological relevance.
The diversity of plant species, the types of plant uses and the estimate of carbon stock in agroforestry system in Harapan Makmur Village, Bengkulu, Indonesia
Authors: WIRYONO WIRYONO , PUTERI VENNY NOVIA UTAMI , SENOAJI GUNGGUNG 
Published: March 2016

Wiryono, Puteri VNU, Senoaji G. 2016. The diversity of plant species, the types of plant uses and the estimate of carbon stock in agroforestry system in Harapan Makmur Village, Bengkulu, Indonesia. Biodiversitas 17: 249-255. Homegardens are a traditional form of agroforestry commonly found in rural areas in Indonesia, where a variety of agricultural crops and forest trees are grown in a mixed system. To some extent, the traditional homegardens resemble natural forest in vegetation structure and composition. The objective of this study was to know the diversity of plant species, the types of plant uses and the estimate of carbon stock in homegardens in, Harapan Makmur Village, Central Bengkulu District, Bengkulu Province, Indonesia. The field work was conducted in 2013. The data of uses were collected through interview, while data on vegetation were gathered from measurement. The data were analyzed qualitatively and quantitatively. The results showed that 101 species of plants were found in the homegardens, with a Shannon-WienerÂ diversity index of 0.99 for trees. The most dominant species of trees was Hevea brasiliensis Willd (rubber tree) with an importance value index of 127 %. For saplings and shrubs, rubber was also the most dominant with 169 individuals, while for herbs, Agrostis sp. was the most dominant species with an average coverage of 25.8 %. The community used plants for several purposes: 41 species for food, 21 for fire wood, 13 for ornamental plants, 11 for medicines, 7 for construction wood, 6 for shade trees, 2 for handy craft, 4 for hedge, 3 for forage, and 2 for coloring. Twenty three species were not used. The estimate of carbon stock in trees was 95.2 ton ha-1.
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