bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multiantigenic DNA Vaccine That Induces Broad Hepatitis C Virus-Specific T-Cell Responses in Mice
Authors: Gummow Jason , Li Yanrui , Yu Wenbo , Garrod Tamsin , Wijesundara Danushka , Brennan Amelia J. , Mullick Ranajoy , Voskoboinik Ilia , Grubor-Bauk Branka , Gowans Eric J. 
Published: May 2015

ABSTRACTThere are 3 to 4 million new hepatitis C virus (HCV) infections annually around the world, but no vaccine is available. Robust T-cell mediated responses are necessary for effective clearance of the virus, and DNA vaccines result in a cell-mediated bias. Adjuvants are often required for effective vaccination, but during natural lytic viral infections damage-associated molecular patterns (DAMPs) are released, which act as natural adjuvants. Hence, a vaccine that induces cell necrosis and releases DAMPs will result in cell-mediated immunity (CMI), similar to that resulting from natural lytic viral infection. We have generated a DNA vaccine with the ability to elicit strong CMI against the HCV nonstructural (NS) proteins (3, 4A, 4B, and 5B) by encoding a cytolytic protein, perforin (PRF), and the antigens on a single plasmid. We examined the efficacy of the vaccines in C57BL/6 mice, as determined by gamma interferon enzyme-linked immunosorbent spot assay, cell proliferation studies, and intracellular cytokine production. Initially, we showed that encoding the NS4A protein in a vaccine which encoded only NS3 reduced the immunogenicity of NS3, whereas including PRF increased NS3 immunogenicity. In contrast, the inclusion of NS4A increased the immunogenicity of the NS3, NS4B, andNS5B proteins, when encoded in a DNA vaccine that also encoded PRF. Finally, vaccines that also encoded PRF elicited similar levels of CMI against each protein after vaccination with DNA encoding NS3, NS4A, NS4B, and NS5B compared to mice vaccinated with DNA encoding only NS3 or NS4B/5B. Thus, we have developed a promising “multiantigen” vaccine that elicits robust CMI.IMPORTANCESince their development, vaccines have reduced the global burden of disease. One strategy for vaccine development is to use commercially viable DNA technology, which has the potential to generate robust immune responses. Hepatitis C virus causes chronic liver infection and is a leading cause of liver cancer. To date, no vaccine is currently available, and treatment is costly and often results in side effects, limiting the number of patients who are treated. Despite recent advances in treatment, prevention remains the key to efficient control and elimination of this virus. Here, we describe a novel DNA vaccine against hepatitis C virus that is capable of inducing robust cell-mediated immune responses in mice and is a promising vaccine candidate for humans.
Identification of Influenza A Virus PB2 Residues Involved in Enhanced Polymerase Activity and Virus Growth in Mammalian Cells at Low Temperatures
Authors: Hayashi Tsuyoshi , Wills Saintedym , Bussey Kendra A. , Takimoto Toru 
Published: May 2015

ABSTRACT
Mutations in the polymerase genes are known to play a major role in avian influenza virus adaptation to mammalian hosts. Despite having avian origin PA and PB2, the 2009 pandemic H1N1 virus (pH1N1) can replicate well in mammalian respiratory tracts, suggesting that these proteins have acquired mutations for efficient growth in humans. We have previously shown that PA from the pH1N1 virus A/California/04/09 (Cal) strongly enhances activity of an otherwise avian polymerase complex derived from A/chicken/Nanchang/3-120/01 (Nan) in mammalian cells. However, this enhancement was observed at 37°C but not at the lower temperature of 34°C. An additional introduction of Cal PB2 enhanced activity at 34°C, suggesting the presence of unidentified residues in Cal PB2 that are required for efficient growth at low temperature. Here, we sought to determine the key PB2 residues which confer enhanced polymerase activity and virus growth in human cells at low temperature. Using a reporter gene assay, we identified novel mutations, PB2 V661A and V683T/A684S, which are involved in enhanced Cal polymerase activity at low temperature. The PB2 T271A mutation, which we previously reported, also contributed to enhanced activity. The growth of recombinant Cal containing PB2 with Nan residues 271T/661V/683V/684A was strongly reduced in human cells compared to wild-type virus at low temperature. Among the four residues, 271A and 684S are conserved in human and pH1N1 viruses but not in avian viruses, suggesting an important role in mammalian adaptation of pH1N1 virus.

IMPORTANCE
The PB2 protein plays a key role in the host adaptation, cold sensitivity, and pathogenesis of influenza A virus. Despite containing an avian origin PB2 lacking the mammalian adaptive mutations 627K or 701N, pH1N1 influenza virus strains can replicate efficiently in the low temperature upper respiratory tract of mammals, suggesting the presence of unknown mutations in the pH1N1 PB2 protein responsible for its low temperature adaptation. Here, in addition to PB2 271A, which has been shown to increase polymerase activity, we identified novel PB2 residues 661A and 683T/684S in pH1N1 which confer enhanced polymerase activity and virus growth in mammalian cells especially at low temperature. Our findings suggest that the presence of these PB2 residues contributes to efficient replication of the pH1N1 virus in the upper respiratory tract, which resulted in efficient human-to-human transmission of this virus.
Human Blood-Circulating Basophils Capture HIV-1 and Mediate Viraltrans-Infection of CD4+T Cells
Authors: Jiang Ai-Ping , Jiang Jin-Feng , Guo Ming-Gao , Jin Yong-Mei , Li Yu-Ye , Wang Jian-Hua 
Published: May 2015

ABSTRACTCell-associated HIV-1 infection has been proposed to play a pivotal role in the spread of HIV-1 infection. Granulocytes are a category of white blood cells, comprising mainly basophils, neutrophils, and eosinophils, and participate in various inflammatory reactions and defense against pathogens. Here, we investigated the role of human blood granulocytes in the dissemination of HIV-1. These cells were found to express a variety of HIV-1 attachment factors (HAFs). Basophils expressed HAFs dendritic cell (DC)-specific intercellular adhesion molecule 3 (ICAM3)-grabbing nonintegrin (DC-SIGN), DC immunoreceptor (DCIR), heparan sulfate proteoglycan (HSPG), and α4β7 integrin and mediated the most efficient capture of HIV-1 on the cell surface. Neutrophils were found to express DCIR and demonstrated limited efficiency of viral capture. Eosinophils expressed α4β7 integrin but exhibited little or no virus-binding capacity. Intriguingly, following direct contact with CD4+T cells, viruses harbored on the surface of basophils were transferred to T cells. The contact between basophils and CD4+T cells and formation of infectious synapses appeared necessary for efficient HIV-1 spread. In HIV-1-infected individuals, the frequency of basophils remained fairly stable over the course of disease, regardless of CD4+T depletion or the emergence of AIDS-associated opportunistic infections. Collectively, our results provide novel insights into the roles of granulocytes, particularly basophils, in HIV-1 dissemination. Thus, strategies designed to prevent basophil-mediated viral capture and transfer may be developed into a new form of therapy.IMPORTANCECell-associated HIV-1 infection has been proposed to play a pivotal role in the spread of HIV-1 infection. Here, we demonstrated that human blood-circulating granulocytes, particularly basophils, can capture HIV-1 and mediate viraltrans-infection of CD4+T cells. The expression of a variety of HIV-1 attachment factors, such as the C-type lectins, etc., facilitates viral capture and transfer. Intriguingly, the frequency of basophils in patients with different levels of CD4+T counts remains fairly stable during the course of disease. Our results provide novel insights into the roles of granulocytes, particularly basophils, in HIV-1 dissemination. We suggest that strategies designed to prevent basophil-mediated viral capture and transfer may be a new direction for the development of anti-HIV therapy.
Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2
Authors: Newman Ruchi M. , Lamers Susanna L. , Weiner Brian , Ray Stuart C. , Colgrove Robert C. , Diaz Fernando , Jing Lichen , Wang Kening , Saif Sakina , Young Sarah , Henn Matthew , Laeyendecker Oliver , Tobian Aaron A. R. , Cohen Jeffrey I. , Koelle David M. , Quinn Thomas C. , Knipe David M. 
Published: May 2015

ABSTRACT
Herpes simplex virus 2 (HSV-2), the principal causative agent of recurrent genital herpes, is a highly prevalent viral infection worldwide. Limited information is available on the amount of genomic DNA variation between HSV-2 strains because only two genomes have been determined, the HG52 laboratory strain and the newly sequenced SD90e low-passage-number clinical isolate strain, each from a different geographical area. In this study, we report the nearly complete genome sequences of 34 HSV-2 low-passage-number and laboratory strains, 14 of which were collected in Uganda, 1 in South Africa, 11 in the United States, and 8 in Japan. Our analyses of these genomes demonstrated remarkable sequence conservation, regardless of geographic origin, with the maximum nucleotide divergence between strains being 0.4% across the genome. In contrast, prior studies indicated that HSV-1 genomes exhibit more sequence diversity, as well as geographical clustering. Additionally, unlike HSV-1, little viral recombination between HSV-2 strains could be substantiated. These results are interpreted in light of HSV-2 evolution, epidemiology, and pathogenesis. Finally, the newly generated sequences more closely resemble the low-passage-number SD90e than HG52, supporting the use of the former as the new reference genome of HSV-2.

IMPORTANCE
Herpes simplex virus 2 (HSV-2) is a causative agent of genital and neonatal herpes. Therefore, knowledge of its DNA genome and genetic variability is central to preventing and treating genital herpes. However, only two full-length HSV-2 genomes have been reported. In this study, we sequenced 34 additional HSV-2 low-passage-number and laboratory viral genomes and initiated analysis of the genetic diversity of HSV-2 strains from around the world. The analysis of these genomes will facilitate research aimed at vaccine development, diagnosis, and the evaluation of clinical manifestations and transmission of HSV-2. This information will also contribute to our understanding of HSV evolution.
Induction of PD-L1 Expression by the EML4–ALK Oncoprotein and Downstream Signaling Pathways in Non–Small Cell Lung Cancer
Authors: Ota Keiichi , Azuma Koichi , Kawahara Akihiko , Hattori Satoshi , Iwama Eiji , Tanizaki Junko , Harada Taishi , Matsumoto Koichiro , Takayama Koichi , Takamori Shinzo , Kage Masayoshi , Hoshino Tomoaki , Nakanishi Yoichi , Okamoto Isamu 
Published: May 2015

Abstract
Purpose: Therapies targeted to the immune checkpoint mediated by PD-1 and PD-L1 show antitumor activity in a subset of patients with non–small cell lung cancer (NSCLC). We have now examined PD-L1 expression and its regulation in NSCLC positive for the EML4–ALK fusion gene.
Experimental Design: The expression of PD-L1 at the protein and mRNA levels in NSCLC cell lines was examined by flow cytometry and by reverse transcription and real-time PCR analysis, respectively. The expression of PD-L1 in 134 surgically resected NSCLC specimens was evaluated by immunohistochemical analysis.
Results: The PD-L1 expression level was higher in NSCLC cell lines positive for EML4–ALK than in those negative for the fusion gene. Forced expression of EML4–ALK in Ba/F3 cells markedly increased PD-L1 expression, whereas endogenous PD-L1 expression in EML4–ALK–positive NSCLC cells was attenuated by treatment with the specific ALK inhibitor alectinib or by RNAi with ALK siRNAs. Furthermore, expression of PD-L1 was downregulated by inhibitors of the MEK–ERK and PI3K–AKT signaling pathways in NSCLC cells positive for either EML4–ALK or activating mutations of the EGFR. Finally, the expression level of PD-L1 was positively associated with the presence of EML4–ALK in NSCLC specimens.
Conclusions: Our findings that both EML4–ALK and mutant EGFR upregulate PD-L1 by activating PI3K–AKT and MEK–ERK signaling pathways in NSCLC reveal a direct link between oncogenic drivers and PD-L1 expression. Clin Cancer Res; 21(17); 4014–21. ©2015 AACR.
RacGAP1 Is a Novel Downstream Effector of E2F7-Dependent Resistance to Doxorubicin and Is Prognostic for Overall Survival in Squamous Cell Carcinoma
Authors: Hazar-Rethinam Mehlika , de Long Lilia Merida , Gannon Orla M. , Boros Samuel , Vargas Ana Cristina , Dzienis Marcin , Mukhopadhyay Pamela , Saenz-Ponce Natalia , Dantzic Daniel D.E. , Simpson Fiona , Saunders Nicholas A. 
Published: May 2015

Abstract
We have previously shown that E2F7 contributes to drug resistance in head and neck squamous cell carcinoma (HNSCC) cells. Considering that dysregulation of responses to chemotherapy-induced cytotoxicity is one of the major reasons for treatment failure in HNSCC, identifying the downstream effectors that regulate E2F7-dependent sensitivity to chemotherapeutic agents may have direct clinical impact. We used transcriptomic profiling to identify candidate pathways that contribute to E2F7-dependent resistance to doxorubicin. We then manipulated the expression of the candidate pathway using overexpression and knockdown in in vitro and in vivo models of SCC to demonstrate causality. In addition, we examined the expression of E2F7 and RacGAP1 in a custom tissue microarray (TMA) generated from HNSCC patient samples. Transcriptomic profiling identified RacGAP1 as a potential mediator of E2F7-dependent drug resistance. We validated E2F7-dependent upregulation of RacGAP1 in doxorubicin-insensitive SCC25 cells. Extending this, we found that selective upregulation of RacGAP1 induced doxorubicin resistance in previously sensitive KJDSV40. Similarly, stable knockdown of RacGAP1 in insensitive SCC25 cells induced sensitivity to doxorubicin in vitro and in vivo. RacGAP1 expression was validated in a TMA, and we showed that HNSCCs that overexpress RacGAP1 are associated with a poorer patient overall survival. Furthermore, E2F7-induced doxorubicin resistance was mediated via RacGAP1-dependent activation of AKT. Finally, we show that SCC cells deficient in RacGAP1 grow slower and are sensitized to the cytotoxic actions of doxorubicin in vivo. These findings identify RacGAP1 overexpression as a novel prognostic marker of survival and a potential target to sensitize SCC to doxorubicin. Mol Cancer Ther; 14(8); 1939–50. ©2015 AACR.
Evaluation of safety and effectiveness of factor VIII treatment in haemophilia A patients with low titre inhibitors or a personal history of inhibitor
Authors: Romanov Vadim , Marcucci Maura , Cheng Ji , Thabane Lehana , Iorio Alfonso 
Published: May 2015

SummaryThere is no prospective evidence on inhibitor recurrence among haemophilia A patients with low titre inhibitors or history of inhibitors, and whether or how therapeutic choices affect the risk of recurrence. The aims of this study were to synthesise safety data in patients with moderate-severe haemophilia A and with low titre inhibitors or inhibitor history enrolled in the rAHF PFM (ADVATE) – Post-Authorization Safety Studies (ADVATE-PASS) international programme. The study was conducted in clinics participating to the ADVATE PASS programme. The patient population consisted of patients entering the studies with low titre (≤5 BU) inhibitors or a positive personal history of inhibitors. Patients on Immune Tolerance Induction at study entry were excluded. Primary outcome was new or recurrent inhibitor titre > 5 BU. Secondary outcomes were any increase of inhibitor titre not reaching 5 BU; any unexplained change in treatment regimen. Primary analysis was done by two-stage random effects meta-analysis. Secondary analysis was done by a hierarchical Bayesian random effects logistic model. A total of 219 patients from seven studies were included. Of these 214 (97.7 %) patients had been previously treated for more than 50 exposure days. Two hundred ten patients had positive history for inhibitors, nine a baseline measurable titre. No patient presented a primary outcome event (95 % confidence interval [CI] 0–1.6 %). Six patients with previous history developed a low titre recurrence (overall rate 2.2, 95 %CI 0–4.8 %). When any increase of inhibitor titre or any treatment change was accounted for, overall 3.7 % (95 % CI 0 %-8.0 %) of patients experienced the outcome. In conclusion, the observed rate of events does not support the definition of this population as at high risk for inhibitor development.
Alchemy in Cambridge
Authors: Timmermann Anke 
Published: May 2015

Alchemy in Cambridge captures the alchemical content of 56 manuscripts in Cambridge, in particular the libraries of Trinity College, Corpus Christi College and St John’s College, the University Library and the Fitzwilliam Museum. As such, this catalogue makes visible a large number of previously unknown or obscured alchemica. While extant bibliographies, including those by M.R. James a century ago, were compiled by polymathic bibliographers for a wide audience of researchers, Alchemy in Cambridge benefits from the substantial developments in the history of alchemy, bibliography, and related scholarship in recent decades. Many texts are here identified for the first time. Another vital feature is the incorporation of information on alchemical illustrations in the manuscripts, intended to facilitate research on the visual culture of alchemy. The catalogue is aimed at historians of alchemy and science, and of high interest to manuscript scholars, historians of art and historians of college and university libraries.
Improving High-Resolution Weather Forecasts Using the Weather Research and Forecasting (WRF) Model with an Updated Kain–Fritsch Scheme
Authors: Zheng Yue , Alapaty Kiran , Herwehe Jerold A. , Del Genio Anthony D. , Niyogi Dev 
Published: May 2015

Abstract
Efforts to improve the prediction accuracy of high-resolution (1–10 km) surface precipitation distribution and variability are of vital importance to local aspects of air pollution, wet deposition, and regional climate. However, precipitation biases and errors can occur at these spatial scales due to uncertainties in initial meteorological conditions and/or grid-scale cloud microphysics schemes. In particular, it is still unclear to what extent a subgrid-scale convection scheme could be modified to bring in scale awareness for improving high-resolution short-term precipitation forecasts in the WRF Model. To address these issues, the authors introduced scale-aware parameterized cloud dynamics for high-resolution forecasts by making several changes to the Kain–Fritsch (KF) convective parameterization scheme in the WRF Model. These changes include subgrid-scale cloud–radiation interactions, a dynamic adjustment time scale, impacts of cloud updraft mass fluxes on grid-scale vertical velocity, and lifting condensation level–based entrainment methodology that includes scale dependency.
A series of 48-h retrospective forecasts using a combination of three treatments of convection (KF, updated KF, and the use of no cumulus parameterization), two cloud microphysics schemes, and two types of initial condition datasets were performed over the U.S. southern Great Plains on 9- and 3-km grid spacings during the summers of 2002 and 2010. Results indicate that 1) the source of initial conditions plays a key role in high-resolution precipitation forecasting, and 2) the authors’ updated KF scheme greatly alleviates the excessive precipitation at 9-km grid spacing and improves results at 3-km grid spacing as well. Overall, the study found that the updated KF scheme incorporated into a high-resolution model does provide better forecasts for precipitation location and intensity.
Cutback management literature in the 1970s and 1980s: taking stock
Authors: Raudla Ringa , Savi Riin , Randma-Liiv Tiina 
Published: May 2015

The main purpose of this article is to take stock of the literature on public sector cutback management in the 1970s and the 1980s, with a specific focus on cutback strategies and the contents of cutbacks. Both theoretical and empirical studies, focusing either on the central or local government level or different policy fields, have been reviewed. The study shows that when governments face cutbacks, they need to address the fundamental choice between across-the-board and targeted cutback strategies. Cutbacks do not occur as one-off single actions but are usually carried out in a number of cutback rounds. The longer-lasting and the more severe is fiscal stress, the more likely it is that the governments will start imposing targeted cuts rather than implementing across-the-board strategies. Looking at the patterns of cutback management in the past is expected to provide useful insights for systematizing the approaches to cutback management and for researching the current crisis. Points for practitioners This article provides an overview of cutback management practices in the 1970s and the 1980s with the expectation that it will contribute to addressing the current fiscal crisis. The pros and cons of targeted versus across-the-board cutback strategies are discussed. The article also looks at various cutback measures including operational cuts (hiring freeze, pay freeze, lay-offs), programme and capital cuts. The study shows that the longer-lasting and the more severe the fiscal stress, the more likely it is that the governments will begin to impose targeted rather than across-the-board cuts. It is found that personnel costs are cut rather reluctantly, and hiring freeze is a dominant measure compared to salary cuts or lay-offs.
Is Language a Factor in the Perception of Foreign Accent Syndrome?
Authors: Jose Linda , Read Jennifer , Miller Nick 
Published: May 2015

Neurogenic foreign accent syndrome (FAS) is diagnosed when listeners perceive speech associated with motor speech impairments as foreign rather than disordered. Speakers with foreign accent syndrome typically have aphasia. It remains unclear how far language changes might contribute to the perception of foreign accent syndrome independent of accent. Judges with and without training in language analysis rated orthographic transcriptions of speech from people with foreign accent syndrome, speech-language disorder and no foreign accent syndrome, foreign accent without neurological impairment and healthy controls on scales of foreignness, normalness and disorderedness. Control speakers were judged as significantly more normal, less disordered and less foreign than other groups. Foreign accent syndrome speakers’ transcriptions consistently profiled most closely to those of foreign speakers and significantly different to speakers with speech-language disorder. On normalness and foreignness ratings there were no significant differences between foreign and foreign accent syndrome speakers. For disorderedness, foreign accent syndrome participants fell midway between foreign speakers and those with speech-language impairment only. Slower rate, more hesitations, pauses within and between utterances influenced judgments, delineating control scripts from others. Word-level syntactic and morphological deviations and reduced syntactic and semantic repertoire linked strongly with foreignness perceptions. Greater disordered ratings related to word fragments, poorly intelligible grammatical structures and inappropriate word selection. Language changes influence foreignness perception. Clinical and theoretical issues are addressed.