bluuebunny/crossref_metadata_2025 huggingface dataset:
Onset of Mediterranean outflow into the North Atlantic
Authors: Hernández-Molina F. Javier , Stow Dorrik A. V. , Alvarez-Zarikian Carlos A. , Acton Gary , Bahr André , Balestra Barbara , Ducassou Emmanuelle , Flood Roger , Flores José-Abel , Furota Satoshi , Grunert Patrick , Hodell David , Jimenez-Espejo Francisco , Kim Jin Kyoung , Krissek Lawrence , Kuroda Junichiro , Li Baohua , Llave Estefania , Lofi Johanna , Lourens Lucas , Miller Madeline , Nanayama Futoshi , Nishida Naohisa , Richter Carl , Roque Cristina , Pereira Hélder , Sanchez Goñi Maria Fernanda , Sierro Francisco J. , Singh Arun Deo , Sloss Craig , Takashimizu Yasuhiro , Tzanova Alexandrina , Voelker Antje , Williams Trevor , Xuan Chuang
Published: June 2014

The when of Mediterranean water outflow

The trickle of water that began to flow from the Mediterranean Sea into the Atlantic Ocean after the opening of the Strait of Gibraltar turned into a veritable flood by the end of the Pliocene 2 to 3 million years ago. It then began to influence large-scale ocean circulation in earnest. Hernández-Molina
et al.
describe marine sediment cores collected by an ocean drilling expedition (see the Perspective by Filippelli). The results reveal a detailed history of the timing of Mediterranean outflow water activity and show how the addition of that warm saline water to the cooler less-salty waters of the Atlantic was related to climate changes, deep ocean circulation, and plate tectonics.

Science
, this issue p.
1244
; see also p.
1228
Measuring the path toward malaria elimination
Authors: Churcher Thomas S. , Cohen Justin M. , Novotny Joseph , Ntshalintshali Nyasatu , Kunene Simon , Cauchemez Simon
Published: June 2014

Developing new targets and milestones from standard surveillance data
The genetics of Mexico recapitulates Native American substructure and affects biomedical traits
Authors: Moreno-Estrada Andrés , Gignoux Christopher R. , Fernández-López Juan Carlos , Zakharia Fouad , Sikora Martin , Contreras Alejandra V. , Acuña-Alonzo Victor , Sandoval Karla , Eng Celeste , Romero-Hidalgo Sandra , Ortiz-Tello Patricia , Robles Victoria , Kenny Eimear E. , Nuño-Arana Ismael , Barquera-Lozano Rodrigo , Macín-Pérez Gastón , Granados-Arriola Julio , Huntsman Scott , Galanter Joshua M. , Via Marc , Ford Jean G. , Chapela Rocío , Rodriguez-Cintron William , Rodríguez-Santana Jose R. , Romieu Isabelle , Sienra-Monge Juan José , Navarro Blanca del Rio , London Stephanie J. , Ruiz-Linares Andrés , Garcia-Herrera Rodrigo , Estrada Karol , Hidalgo-Miranda Alfredo , Jimenez-Sanchez Gerardo , Carnevale Alessandra , Soberón Xavier , Canizales-Quinteros Samuel , Rangel-Villalobos Héctor , Silva-Zolezzi Irma , Burchard Esteban Gonzalez , Bustamante Carlos D.
Published: June 2014

The population structure of Native Mexicans

The genetics of indigenous Mexicans exhibit substantial geographical structure, some as divergent from each other as are existing populations of Europeans and Asians. By performing genome-wide analyses on Native Mexicans from differing populations, Moreno-Estrada
et al.
successfully recapitulated the pre-Columbian substructure of Mexico. This ancestral structure is evident among cosmopolitan Mexicans and is correlated with subcontinental origins and medically relevant aspects of lung function. These findings exemplify the importance of understanding the genetic contributions of admixed individuals.

Science
, this issue p.
1280
Asynchronous therapy restores motor control by rewiring of the rat corticospinal tract after stroke
Authors: Wahl A. S. , Omlor W. , Rubio J. C. , Chen J. L. , Zheng H. , Schröter A. , Gullo M. , Weinmann O. , Kobayashi K. , Helmchen F. , Ommer B. , Schwab M. E.
Published: June 2014

Improving stroke recovery by timing treatment

Patients recovering from strokes often fight a long uphill battle, with mixed results. Studying the effect of physical training on regeneration from damaged nerves in a model of stroke in rats, Wahl
et al.
show that timing matters. First, the researchers gave the rats a stroke, which damaged their ability to reach for food pellets with their forelimbs. The researchers then gave them physical training and treated them with an antibody to encourage neural regeneration. The rats improved more when the researchers waited until after the antibody treatment to start the training. Damaged circuits, it seems, need a little time to regrow before being called into action.

Science
, this issue p.
1250
Dehydration melting at the top of the lower mantle
Authors: Schmandt Brandon , Jacobsen Steven D. , Becker Thorsten W. , Liu Zhenxian , Dueker Kenneth G.
Published: June 2014

Cycling water through the transition zone

The water cycle involves more than just the water that circulates between the atmosphere, oceans, and surface waters. It extends deep into Earth's interior as the oceanic crust subducts, or slides, under adjoining plates of crust and sinks into the mantle, carrying water with it. Schmandt
et al.
combined seismological observations beneath North America with geodynamical modeling and high-pressure and -temperature melting experiments. They conclude that the mantle transition zone—410 to 660 km below Earth's surface—acts as a large reservoir of water.

Science
, this issue p.
1265
Comment on “Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA”
Authors: Chisari Francis V. , Mason William S. , Seeger Christoph
Published: June 2014

Lucifora
et al
. (Research Articles, 14 March 2014, p. 1221) report that the hepatitis B virus (HBV) transcriptional template, a long-lived covalently closed circular DNA (cccDNA) molecule, is degraded noncytolytically by agents that up-regulate APOBEC3A and 3B. If these results can be independently confirmed, they would represent a critical first step toward development of a cure for the 400 million patients who are chronically infected by HBV.
The quantum nondemolition derby
Authors: Bouwmeester Dirk
Published: June 2014

Monitored resonators can evade back-action from shot noise in the detection laser

[Also see Report by

Suh
et al.

]
Gary Becker (1930–2014)
Authors: Glaeser Edward L. , Shleifer Andrei
Published: June 2014

An economist used sociology and economics to examine life and explain human behavior
Dinosaur metabolism neither hot nor cold, but just right
Authors: Balter Michael
Published: June 2014

Growth rates suggest answer to long debate: Dinosaurs were “mesothermic,” like today's tuna and echidna.
Legal highs make Uruguay a beacon for marijuana research
Authors: Wade Lizzie
Published: June 2014

Government funds new lab to study the biochemistry and medical uses of the drug.
Strong male bias drives germline mutation in chimpanzees
Authors: Venn Oliver , Turner Isaac , Mathieson Iain , de Groot Natasja , Bontrop Ronald , McVean Gil
Published: June 2014

Male chimps evolve faster with age

Chimpanzees are evolving faster than humans. Venn
et al.
examined the genetics of three generations of western chimpanzees and found that overall the mutation rate is similar between humans and chimpanzees. However, while male humans had three to four times the mutation rate of females, in chimpanzees the sex difference was even higher, with a male mutation rate five to six times that of females. Blame aging dads. For every extra year of the father's age, baby chimpanzees exhibited approximately one extra mutation. This finding will inform future studies of primate evolution.

Science
, this issue p.
1272
LIFE SCIENCE TECHNOLOGIES: Big biological impacts from big data
Authors: May Mike
Published: June 2014

In the life sciences, data can come in many forms, including information about genomic sequences, molecular pathways, and different populations of people. Those data create a potential bonanza, if scientists can overcome one stumbling block: how to handle the complexity of information. Tools and techniques for analyzing big data promise to mold massive mounds of information into a better understanding of the basic biological mechanisms and how the results can be applied in, for example, health care.
Chitinase 3–Like 1 Suppresses Injury and Promotes Fibroproliferative Responses in Mammalian Lung Fibrosis
Authors: Zhou Yang , Peng Hong , Sun Huanxing , Peng Xueyan , Tang Chuyan , Gan Ye , Chen Xiaosong , Mathur Aditi , Hu Buqu , Slade Martin D. , Montgomery Ruth R. , Shaw Albert C. , Homer Robert J. , White Eric S. , Lee Chang-Min , Moore Meagan W. , Gulati Mridu , Geun Lee Chun , Elias Jack A. , Herzog Erica L.
Published: June 2014

Chitinase 3–like 1 protects against lung injury but has a profibrotic role during the repair phase.
Alkylphosphocholine Analogs for Broad-Spectrum Cancer Imaging and Therapy
Authors: Weichert Jamey P. , Clark Paul A. , Kandela Irawati K. , Vaccaro Abram M. , Clarke William , Longino Marc A. , Pinchuk Anatoly N. , Farhoud Mohammed , Swanson Kyle I. , Floberg John M. , Grudzinski Joseph , Titz Benjamin , Traynor Anne M. , Chen Hong-En , Hall Lance T. , Pazoles Christopher J. , Pickhardt Perry J. , Kuo John S.
Published: June 2014

Tumor-specific alkylphosphocholine analogs were evaluated as imaging and therapy agents in patients and in animal models of human cancer.
From Knowledge to Policy: Lessons from Africa
Authors: Nabyonga Juliet , Orem Jackson
Published: June 2014

Partnerships that focus on the research and implementation of low-tech innovations can help to meet health care delivery challenges in low-income countries.
Straight Shooters: Peptibodies Take Aim
Authors: Stephan Matthias
Published: June 2014

Peptide antibodies (peptibodies) aim for and selectively deplete myeloid immune suppressor cells, leading to retarded tumor growth in mice.
Nonneutralizing Functional Antibodies: a New “Old” Paradigm for HIV Vaccines
Authors: Excler Jean-Louis , Ake Julie , Robb Merlin L. , Kim Jerome H. , Plotkin Stanley A.
Published: June 2014

Animal and human data from various viral infections and vaccine studies suggest that nonneutralizing antibodies (nNAb) without neutralizing activityin vitromay play an important role in protection against viral infectionin vivo. This was illustrated by the recent human immunodeficiency virus (HIV) RV144 vaccine efficacy trial, which demonstrated that HIV-specific IgG-mediated nNAb directed against the V2 loop of HIV type 1 envelope (Env) were inversely correlated with risk for HIV acquisition, while Env-specific plasma IgA-mediated antibodies were directly correlated with risk. However, tier 1 NAb in the subset of responders with a low level of plasma Env-specific IgA correlated with decreased risk. Nonhuman primate simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus (SHIV) challenge studies suggest that Env-mediated antibodies are essential and sufficient for protection. A comparison of immune responses generated in human efficacy trials reveals subtle differences in the fine specificities of the antibody responses, in particular in HIV-specific IgG subclasses. The underlying mechanisms that may have contributed to protection against HIV acquisition in humans, although not fully understood, are possibly mediated by antibody-dependent cell-mediated cytotoxicity (ADCC) and/or other nonneutralizing humoral effector functions, such as antibody-mediated phagocytosis. The presence of such functional nNAb in mucosal tissues and cervico-vaginal and rectal secretions challenges the paradigm that NAb are the predominant immune response conferring protection, although this does not negate the desirability of evoking neutralizing antibodies through vaccination. Instead, NAb and nNAb should be looked upon as complementary or synergistic humoral effector functions. Several HIV vaccine clinical trials to study these antibody responses in various prime-boost modalities in the systemic and mucosal compartments are ongoing. The induction of high-frequency HIV-specific functional nNAb at high titers may represent an attractive hypothesis-testing strategy in future HIV vaccine efficacy trials.
Acute Mastoiditis in the Pneumococcal Conjugate Vaccine Era
Authors: Tamir Sharon Ovnat , Roth Yehudah , Dalal Ilan , Goldfarb Abraham , Marom Tal
Published: June 2014

Following the introduction of the 7- and 13-valent pneumococcal conjugate vaccines, we observed an inverse relationship between the increasing rate of immunized children and the proportion of middle ear fluid cultures collected during acute mastoiditis episodes that tested positive forStreptococcus pneumoniaeamong a subset of children 0 to 6 years old who had initially presented with severe acute otitis media and had bacterial cultures collected during tympanocentesis or from spontaneous otorrhea.
A Single B-Repeat of Staphylococcus epidermidis Accumulation-Associated Protein Induces Protective Immune Responses in an Experimental Biomaterial-Associated Infection Mouse Model
Authors: Yan Lin , Zhang Lei , Ma Hongyan , Chiu David , Bryers James D.
Published: June 2014

Nosocomial infections are the fourth leading cause of morbidity and mortality in the United States, resulting in 2 million infections and ∼100,000 deaths each year. More than 60% of these infections are associated with some type of biomedical device.Staphylococcus epidermidisis a commensal bacterium of the human skin and is the most common nosocomial pathogen infecting implanted medical devices, especially those in the cardiovasculature.S. epidermidisantibiotic resistance and biofilm formation on inert surfaces make these infections hard to treat. Accumulation-associated protein (Aap), a cell wall-anchored protein ofS. epidermidis, is considered one of the most important proteins involved in the formation ofS. epidermidisbiofilm. A small recombinant protein vaccine comprising a single B-repeat domain (Brpt1.0) ofS. epidermidisRP62A Aap was developed, and the vaccine's efficacy was evaluatedin vitrowith a biofilm inhibition assay andin vivoin a murine model of biomaterial-associated infection. A high IgG antibody response againstS. epidermidisRP62A was detected in the sera of the mice after two subcutaneous immunizations with Brpt1.0 coadministered with Freund's adjuvant. Sera from Brpt1.0-immunized mice inhibitedin vitroS. epidermidisRP62A biofilm formation in a dose-dependent pattern. After receiving two immunizations, each mouse was surgically implanted with a porous scaffold disk containing 5 × 106CFU ofS. epidermidisRP62A. Weight changes, inflammatory markers, and histological assay results after challenge withS. epidermidisindicated that the mice immunized with Brpt1.0 exhibited significantly higher resistance toS. epidermidisRP62A implant infection than the control mice. Day 8 postchallenge, there was a significantly lower number of bacteria in scaffold sections and surrounding tissues and a lower residual inflammatory response to the infected scaffold disks for the Brpt1.0-immunized mice than for of the ovalbumin (Ova)-immunized mice.
Rapid Detection and Simultaneous Antibiotic Susceptibility Analysis of Yersinia pestis Directly from Clinical Specimens by Use of Reporter Phage
Authors: Vandamm J. P. , Rajanna C. , Sharp N. J. , Molineux I. J. , Schofield D. A.
Published: June 2014

Yersinia pestis
is a tier 1 agent due to its contagious pneumopathogenicity, extremely rapid progression, and high mortality rate. As the disease is usually fatal without appropriate therapy, rapid detection from clinical matrices is critical to patient outcomes. We previously engineered the diagnostic phage ΦA1122 with
luxAB
to create a “light-tagged” reporter phage. ΦA1122::
luxAB
rapidly detects
Y. pestis
in pure culture and human serum by transducing a bioluminescent signal response. In this report, we assessed the analytical specificity of the reporter phage and investigated diagnostic utility (detection and antibiotic susceptibility analysis) directly from spiked whole blood. The bioreporter displayed 100% (
n
= 59) inclusivity for
Y. pestis
and consistent intraspecific signal transduction levels. False positives were not obtained from species typically associated with bacteremia or those relevant to plague diagnosis. However, some non-
pestis Yersinia
strains and
Enterobacteriaceae
did elicit signals, albeit at highly attenuated transduction levels. Diagnostic performance was assayed in simple broth-enriched blood samples and standard aerobic culture bottles. In blood, <10
2
CFU/ml was detected within 5 h. In addition,
Y. pestis
was identified directly from positive blood cultures within 20 to 45 min without further processing. Importantly, coincubation of blood samples with antibiotics facilitated simultaneous antimicrobial susceptibility profiling. Consequently, the reporter phage demonstrated rapid detection and antibiotic susceptibility profiling directly from clinical samples, features that may improve patient prognosis during plague outbreaks.
Interlaboratory Comparison of Sample Preparation Methods, Database Expansions, and Cutoff Values for Identification of Yeasts by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Using a Yeast Test Panel
Authors: Vlek Anneloes , Kolecka Anna , Khayhan Kantarawee , Theelen Bart , Groenewald Marizeth , Boel Edwin ,   Multicenter Study Group, Boekhout Teun
Published: June 2014

An interlaboratory study using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) to determine the identification of clinically important yeasts (
n
= 35) was performed at 11 clinical centers, one company, and one reference center using the Bruker Daltonics MALDI Biotyper system. The optimal cutoff for the MALDI-TOF MS score was investigated using receiver operating characteristic (ROC) curve analyses. The percentages of correct identifications were compared for different sample preparation methods and different databases. Logistic regression analysis was performed to analyze the association between the number of spectra in the database and the percentage of strains that were correctly identified. A total of 5,460 MALDI-TOF MS results were obtained. Using all results, the area under the ROC curve was 0.95 (95% confidence interval [CI], 0.94 to 0.96). With a sensitivity of 0.84 and a specificity of 0.97, a cutoff value of 1.7 was considered optimal. The overall percentage of correct identifications (formic acid-ethanol extraction method, score ≥ 1.7) was 61.5% when the commercial Bruker Daltonics database (BDAL) was used, and it increased to 86.8% by using an extended BDAL supplemented with a Centraalbureau voor Schimmelcultures (CBS)-KNAW Fungal Biodiversity Centre in-house database (BDAL+CBS in-house). A greater number of main spectra (MSP) in the database was associated with a higher percentage of correct identifications (odds ratio [OR], 1.10; 95% CI, 1.05 to 1.15;
P
< 0.01). The results from the direct transfer method ranged from 0% to 82.9% correct identifications, with the results of the top four centers ranging from 71.4% to 82.9% correct identifications. This study supports the use of a cutoff value of 1.7 for the identification of yeasts using MALDI-TOF MS. The inclusion of enough isolates of the same species in the database can enhance the proportion of correctly identified strains. Further optimization of the preparation methods, especially of the direct transfer method, may contribute to improved diagnosis of yeast-related infections.
Time between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections
Authors: Cuthbertson Leah , Rogers Geraint B. , Walker Alan W. , Oliver Anna , Hafiz Tarana , Hoffman Lucas R. , Carroll Mary P. , Parkhill Julian , Bruce Kenneth D. , van der Gast Christopher J.
Published: June 2014

Spontaneously expectorated sputum is traditionally used as the sampling method for the investigation of lower airway infections. While guidelines exist for the handling of these samples for culture-based diagnostic microbiology, there is no comparable consensus on their handling prior to culture-independent analysis. The increasing incorporation of culture-independent approaches in diagnostic microbiology means that it is of critical importance to assess potential biases. The aim of this study was to assess the impact of delayed freezing on culture-independent microbiological analyses and to identify acceptable parameters for sample handling. Sputum samples from eight adult cystic fibrosis (CF) patients were collected and aliquoted into sterile Bijou bottles. Aliquots were stored at room temperature before being frozen at −80°C for increasing intervals, up to a 72-h period. Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions. Substantial variation was observed in samples with high-diversity bacterial communities over time, whereas little variation was observed in low-diversity communities dominated by recognized CF pathogens, regardless of time to freezing. Partitioning into common and rare species demonstrated that the rare species drove changes in similarity. The percentage abundance of anaerobes over the study significantly decreased after 12 h at room temperature (
P
= 0.008). Failure to stabilize samples at −80°C within 12 h of collection results in significant changes in the detected community composition.
Quality Control MIC Ranges Used for Telavancin with Application of a Revised CLSI Reference Broth Microdilution Method
Authors: Ross James E. , Mendes Rodrigo E. , Jones Ronald N.
Published: June 2014

The telavancin broth microdilution susceptibility testing method was revised, which provides MIC results lower than those obtained by the previous method. This study was performed to reestablish the quality control ranges for telavancin when tested against the strains (updated MIC range)
Staphylococcus aureus
ATCC 29213 (0.03 to 0.12 μg/ml),
Enterococcus faecalis
ATCC 29212 (0.03 to 0.12 μg/ml), and
Streptococcus pneumoniae
ATCC 49619 (0.004 to 0.015 μg/ml).
A Novel Mode of Poxvirus Superinfection Exclusion That Prevents Fusion of the Lipid Bilayers of Viral and Cellular Membranes
Authors: Laliberte Jason P. , Moss Bernard
Published: June 2014

Superinfection exclusion is a widespread phenomenon that prevents secondary infections by closely related viruses. The vaccinia virus A56 and K2 proteins in the cell membrane can prevent superinfection by interacting with the entry-fusion complex of subsequent viruses. Here, we described another form of exclusion that is established earlier in infection and does not require the A56 or K2 protein. Cells infected with one or more infectious virions excluded hundreds of superinfecting vaccinia virus particles. A related orthopoxvirus, but neither a flavivirus nor a rhabdovirus, was also excluded, indicating selectivity. Although superinfecting vaccinia virus bound to cells, infection was inhibited at the membrane fusion step, thereby preventing core entry into the cytoplasm and early gene expression. In contrast, A56/K2 protein-mediated exclusion occurred subsequent to membrane fusion. Induction of resistance to superinfection depended on viral RNA and protein synthesis by the primary virus but did not require DNA replication. Although superinfection resistance correlated with virus-induced changes in the cytoskeleton, studies with mutant vaccinia viruses indicated that the cytoskeletal changes were not necessary for resistance to superinfection. Interferon-inducible transmembrane proteins, which can inhibit membrane fusion in other viral systems, did not prevent vaccinia virus membrane fusion, suggesting that these interferon-inducible proteins are not involved in superinfection exclusion. While the mechanism remains to be determined, the early establishment of superinfection exclusion may provide a “winner-take-all” reward to the first poxvirus particles that successfully initiate infection and prevent the entry and genome reproduction of defective or less fit particles.

IMPORTANCE
The replication of a virus usually follows a defined sequence of events: attachment, entry into the cytoplasm or nucleus, gene expression, genome replication, assembly of infectious particles, and spread to other cells. Although multiple virus particles may enter a cell at the same time, mechanisms exist to prevent infection by subsequent viruses. The latter phenomenon, known as superinfection exclusion, can occur by a variety of mechanisms that are not well understood. We showed that superinfection by vaccinia virus was prevented at the membrane fusion step, which closely followed virion attachment. Thus, neither gene expression nor genome replication of the superinfecting virus occurred. Expression of early proteins by the primary virus was necessary and sufficient to induce the superinfection-resistant state. Superinfection exclusion may be beneficial to vaccinia virus by selecting particles that can infect cells rapidly, excluding defective particles and synchronizing the replication cycle.
Intranasal Adenovirus-Vectored Vaccine for Induction of Long-Lasting Humoral Immunity-Mediated Broad Protection against Influenza in Mice
Authors: Kim Eun Hye , Park Hae-Jung , Han Gye-Yeong , Song Man-Ki , Pereboev Alexander , Hong Jeong S. , Chang Jun , Byun Young-Ho , Seong Baik Lin , Nguyen Huan H.
Published: June 2014

Influenza vaccines aimed at inducing antibody (Ab) responses against viral surface hemagglutinin (HA) and neuraminidase (NA) provide sterile immunity to infection with the same subtypes. Vaccines targeting viral conserved determinants shared by the influenza A viruses (IAV) offer heterosubtypic immunity (HSI), a broad protection against different subtypes. We proposed that vaccines targeting both HA and the conserved ectodomain of matrix protein 2 (M2e) would provide protection against infection with the same subtype and also HSI against other subtypes. We report here that single intranasal immunization with a recombinant adenovirus (rAd) vector encoding both HA of H5 virus and M2e (rAdH5/M2e) induced significant HA- and M2e-specific Ab responses, along with protection against heterosubtypic challenge in mice. The protection is superior compared to that induced by rAd vector encoding either HA (rAdH5), or M2e (rAdM2e). While protection against homotypic H5 virus is primarily mediated by virus-neutralizing Abs, the cross-protection is associated with Abs directed to conserved stalk HA and M2e that seem to have an additive effect. Consistently, adoptive transfer of antisera induced by rAdH5/M2e provided the best protection against heterosubtypic challenge compared to that provided by antisera derived from mice immunized with rAdH5 or rAdM2e. These results support the development of rAd-vectored vaccines encoding both H5 and M2e as universal vaccines against different IAV subtypes.

IMPORTANCECurrent licensed influenza vaccines provide protection limited to the infection with same virus strains; therefore, the composition of influenza vaccines has to be revised every year. We have developed a new universal influenza vaccine that is highly efficient in induction of long-lasting cross-protection against different influenza virus strains. The cross-protection is associated with a high level of vaccine-induced antibodies against the conserved stalk domain of influenza virus hemagglutinin and the ectodomain of matrix protein. The vaccine could be used to stimulate cross-protective antibodies for the prevention and treatment of influenza with immediate effect for individuals who fail to respond to or receive the vaccine in due time. The vaccine offers a new tool to control influenza outbreaks, including pandemics.
Unfixed Endogenous Retroviral Insertions in the Human Population
Authors: Marchi Emanuele , Kanapin Alex , Magiorkinis Gkikas , Belshaw Robert
Published: June 2014

One lineage of human endogenous retroviruses (HERVs), HERV-K(HML2), is upregulated in many cancers, some autoimmune/inflammatory diseases, and HIV-infected cells. Despite 3 decades of research, it is not known if these viruses play a causal role in disease, and there has been recent interest in whether they can be used as immunotherapy targets. Resolution of both these questions will be helped by an ability to distinguish between the effects of different integrated copies of the virus (loci). Research so far has concentrated on the 20 or so recently integrated loci that, with one exception, are in the human reference genome sequence. However, this viral lineage has been copying in the human population within the last million years, so some loci will inevitably be present in the human population but absent from the reference sequence. We therefore performed the first detailed search for such loci by mining whole-genome sequences generated by next-generation sequencing. We found a total of 17 loci, and the frequency of their presence ranged from only 2 of the 358 individuals examined to over 95% of them. On average, each individual had six loci that are not in the human reference genome sequence. Comparing the number of loci that we found to an expectation derived from a neutral population genetic model suggests that the lineage was copying until at least ∼250,000 years ago.

IMPORTANCE
About 5% of the human genome sequence is composed of the remains of retroviruses that over millions of years have integrated into the chromosomes of egg and/or sperm precursor cells. There are indications that protein expression of these viruses is higher in some diseases, and we need to know (i) whether these viruses have a role in causing disease and (ii) whether they can be used as immunotherapy targets in some of them. Answering both questions requires a better understanding of how individuals differ in the viruses that they carry. We carried out the first careful search for new viruses in some of the many human genome sequences that are now available thanks to advances in sequencing technology. We also compared the number that we found to a theoretical expectation to see if it is likely that these viruses are still replicating in the human population today.
Rewiring of Cellular Membrane Homeostasis by Picornaviruses
Authors: Belov George A. , Sztul Elizabeth
Published: June 2014

Viruses are obligatory intracellular parasites and utilize host elements to support key viral processes, including penetration of the plasma membrane, initiation of infection, replication, and suppression of the host's antiviral defenses. In this review, we focus on picornaviruses, a family of positive-strand RNA viruses, and discuss the mechanisms by which these viruses hijack the cellular machinery to form and operate membranous replication complexes. Studies aimed at revealing factors required for the establishment of viral replication structures identified several cellular-membrane-remodeling proteins and led to the development of models in which the virus used a preexisting cellular-membrane-shaping pathway “as is” for generating its replication organelles. However, as more data accumulate, this view is being increasingly questioned, and it is becoming clearer that viruses may utilize cellular factors in ways that are distinct from the normal functions of these proteins in uninfected cells. In addition, the proteincentric view is being supplemented by important new studies showing a previously unappreciated deep remodeling of lipid homeostasis, including extreme changes to phospholipid biosynthesis and cholesterol trafficking. The data on viral modifications of lipid biosynthetic pathways are still rudimentary, but it appears once again that the viruses may rewire existing pathways to generate novel functions. Despite remarkable progress, our understanding of how a handful of viral proteins can completely overrun the multilayered, complex mechanisms that control the membrane organization of a eukaryotic cell remains very limited.
Human Cytomegalovirus Modulates Monocyte-Mediated Innate Immune Responses during Short-Term Experimental LatencyIn Vitro
Authors: Noriega Vanessa M. , Haye Kester K. , Kraus Thomas A. , Kowalsky Shanna R. , Ge Yongchao , Moran Thomas M. , Tortorella Domenico
Published: June 2014

The ability of human cytomegalovirus (HCMV) to establish lifelong persistence and reactivate from latency is critical to its success as a pathogen. Here we describe a short-termin vitromodel representing the events surrounding HCMV latency and reactivation in circulating peripheral blood monocytes that was developed in order to study the immunological consequence of latent virus carriage. Infection of human CD14+monocytes by HCMV resulted in the immediate establishment of latency, as evidenced by the absence of particular lytic gene expression, the transcription of latency-associated mRNAs, and the maintenance of viral genomes. Latent HCMV induced cellular differentiation to a macrophage lineage, causing production of selective proinflammatory cytokines and myeloid-cell chemoattractants that most likely play a role in virus dissemination in the host. Analysis of global cellular gene expression revealed activation of innate immune responses and the modulation of protein and lipid synthesis to accommodate latent HCMV infection. Remarkably, monocytes harboring latent virus exhibited selective responses to secondary stimuli known to induce an antiviral state. Furthermore, when challenged with type I and II interferon, latently infected cells demonstrated a blockade of signaling at the level of STAT1 phosphorylation. The data demonstrate that HCMV reprograms specific cellular pathways in monocytes, most notably innate immune responses, which may play a role in the establishment of, maintenance of, and reactivation from latency. The modulation of innate immune responses is likely a viral evasion strategy contributing to viral dissemination and pathogenesis in the host.

IMPORTANCEHCMV has the ability to establish a lifelong infection within the host, a phenomenon termed latency. We have established a short-term model system in human peripheral blood monocytes to study the immunological relevance of latent virus carriage. Infection of CD14+monocytes by HCMV results in the generation of latency-specific transcripts, maintenance of viral genomes, and the capacity to reenter the lytic cycle. During short-term latency in monocytes the virus initiates a program of differentiation to inflammatory macrophages that coincides with the modulation of cytokine secretion and specific cellular processes. HCMV-infected monocytes are hindered in their capacity to exert normal immunoprotective mechanisms. Additionally, latent virus disrupts type I and II interferon signaling at the level of STAT1 phosphorylation. Thisin vitromodel system can significantly contribute to our understanding of the molecular and inflammatory factors that initiate HCMV reactivation in the host and allow the development of strategies to eradicate virus persistence.
Influenza Virus Infectivity and Virulence following Ocular-Only Aerosol Inoculation of Ferrets
Authors: Belser Jessica A. , Gustin Kortney M. , Katz Jacqueline M. , Maines Taronna R. , Tumpey Terrence M.
Published: June 2014

Respiratory pathogens have traditionally been studied by examining the exposure and infection of respiratory tract tissues. However, these studies typically overlook the role of ocular surfaces, which represent both a potential site of virus replication and a portal of entry for the establishment of a respiratory infection. To model transocular virus entry in a mammalian species, we established a novel inoculation method that delivers an aerosol inoculum exclusively to the ferret ocular surface. Using influenza virus as a representative respiratory pathogen, we found that both human and avian viruses mounted productive respiratory infections in ferrets following ocular-only aerosol inoculation, and we demonstrated that H5N1 virus can result in a fatal infection at doses below 10 PFU or with exposure times as short as 2 min. Ferrets inoculated by the ocular aerosol route with an avian (H7N7, H7N9) or human (H1N1, H3N2v) virus were capable of transmitting the virus to naïve animals in direct-contact or respiratory-droplet models, respectively. Our results reveal that ocular-only exposure to virus-containing aerosols constitutes a valid exposure route for a potentially fatal respiratory infection, even for viruses that do not demonstrate an ocular tropism, underscoring the public health implications of ocular exposure in clinical or occupational settings.

IMPORTANCE
In the absence of eye protection, the human ocular surface remains vulnerable to infection with aerosolized respiratory viruses. In this study, we present a way to inoculate laboratory mammals that excludes respiratory exposure, infecting ferrets only by ocular exposure to influenza virus-containing aerosols. This study demonstrates that the use of respiratory protection alone does not fully protect against influenza virus exposure, infection, and severe disease.
Intranasal P Particle Vaccine Provided Partial Cross-Variant Protection against Human GII.4 Norovirus Diarrhea in Gnotobiotic Pigs
Authors: Kocher Jacob , Bui Tammy , Giri-Rachman Ernawati , Wen Ke , Li Guohua , Yang Xingdong , Liu Fangning , Tan Ming , Xia Ming , Zhong Weiming , Jiang Xi , Yuan Lijuan
Published: June 2014

Noroviruses (NoVs) are the leading cause of nonbacterial acute gastroenteritis worldwide in people of all ages. The P particle is a novel vaccine candidate derived from the protruding (P) domain of the NoV VP1 capsid protein. This study utilized the neonatal gnotobiotic pig model to evaluate the protective efficacies of primary infection, P particles, and virus-like particles (VLPs) against NoV infection and disease and the T cell responses to these treatments. Pigs either were vaccinated intranasally with GII.4/1997 NoV (VA387)-derived P particles or VLPs or were inoculated orally with a GII.4/2006b NoV variant. At postinoculation day (PID) 28, pigs either were euthanized or were challenged with the GII.4/2006b variant and monitored for diarrhea and virus shedding for 7 days. The T cell responses in intestinal and systemic lymphoid tissues were examined. Primary NoV infection provided 83% homologous protection against diarrhea and 49% homologous protection against virus shedding, while the P particle and VLP vaccines provided cross-variant protection (47% and 60%, respectively) against diarrhea. The protection rates against diarrhea are significantly inversely correlated with T cell expansion in the duodenum and are positively correlated with T cell expansion in the ileum and spleen. The P particle vaccine primed for stronger immune responses than VLPs, including significantly higher numbers of activated CD4
+
T cells in all tissues, gamma interferon-producing (IFN-γ
+
) CD8
+
T cells in the duodenum, regulatory T cells (Tregs) in the blood, and transforming growth factor β (TGF-β)-producing CD4
+
CD25
−
FoxP3
+
Tregs in the spleen postchallenge, indicating that P particles are more immunogenic than VLPs at the same dose. In conclusion, the P particle vaccine is a promising vaccine candidate worthy of further development.

IMPORTANCE
The norovirus (NoV) P particle is a vaccine candidate derived from the protruding (P) domain of the NoV VP1 capsid protein. P particles can be easily produced in
Escherichia coli
at high yields and thus may be more economically viable than the virus-like particle (VLP) vaccine. This study demonstrated, for the first time, the cross-variant protection (46.7%) of the intranasal P particle vaccine against human NoV diarrhea and revealed in detail the intestinal and systemic T cell responses by using the gnotobiotic pig model. The cross-variant protective efficacy of the P particle vaccine was comparable to that of the VLP vaccine in pigs (60%) and to the homologous protective efficacy of the VLP vaccine in humans (47%). NoV is now the leading cause of pediatric dehydrating diarrhea, responsible for approximately 1 million hospital visits for U.S. children and 218,000 deaths in developing countries. The P particle vaccine holds promise for reducing the disease burden and mortality.
The Herpes Simplex Virus 1 Virion Host Shutoff Protein Enhances Translation of Viral Late mRNAs by Preventing mRNA Overload
Authors: Dauber Bianca , Saffran Holly A. , Smiley James R.
Published: June 2014

We recently demonstrated that the virion host shutoff (vhs) protein, an mRNA-specific endonuclease, is required for efficient herpes simplex virus 1 (HSV-1) replication and translation of viral true-late mRNAs, but not other viral and cellular mRNAs, in many cell types (B. Dauber, J. Pelletier, and J. R. Smiley, J. Virol. 85:5363–5373, 2011,
http://dx.doi.org/10.1128/JVI.00115-11
). Here, we evaluated whether the structure of true-late mRNAs or the timing of their transcription is responsible for the poor translation efficiency in the absence of vhs. To test whether the highly structured 5′ untranslated region (5′UTR) of the true-late gC mRNA is the primary obstacle for translation initiation, we replaced it with the less structured 5′UTR of the γ-actin mRNA. However, this mutation did not restore translation in the context of a vhs-deficient virus. We then examined whether the timing of transcription affects translation efficiency at late times. To this end, we engineered a vhs-deficient virus mutant that transcribes the true-late gene US11 with immediate-early kinetics (IEUS11-ΔSma). Interestingly, IEUS11-ΔSma showed increased translational activity on the US11 transcript at late times postinfection, and US11 protein levels were restored to wild-type levels. These results suggest that mRNAs can maintain translational activity throughout the late stage of infection if they are present before translation factors and/or ribosomes become limiting. Taken together, these results provide evidence that in the absence of the mRNA-destabilizing function of vhs, accumulation of viral mRNAs overwhelms the capacity of the host translational machinery, leading to functional exclusion of the last mRNAs that are made during infection.

IMPORTANCE
The process of mRNA translation accounts for a significant portion of a cell's energy consumption. To ensure efficient use of cellular resources, transcription, translation, and mRNA decay are tightly linked and highly regulated. However, during virus infection, the overall amount of mRNA may increase drastically, possibly overloading the capacity of the translation apparatus. Our results suggest that the HSV-1 vhs protein, an mRNA-specific endoribonuclease, prevents mRNA overload during infection, thereby allowing translation of late viral mRNAs. The requirement for vhs varies between cell types. Further studies of the basis for this difference likely will offer insights into how cells regulate overall mRNA levels and access to the translational apparatus.
STAT4 Deficiency Fails To Induce Lung Th2 or Th17 Immunity following Primary or Secondary Respiratory Syncytial Virus (RSV) Challenge but Enhances the Lung RSV-Specific CD8
+
T Cell Immune Response to Secondary Challenge
Authors: Dulek Daniel E. , Newcomb Dawn C. , Toki Shinji , Goliniewska Kasia , Cephus Jacqueline , Reiss Sara , Bates John T. , Crowe James E. , Boyd Kelli L. , Moore Martin L. , Zhou Weisong , Peebles R. Stokes
Published: June 2014

Immune-mediated lung injury is a hallmark of lower respiratory tract illness caused by respiratory syncytial virus (RSV). STAT4 plays a critical role in CD4
+
Th1 lineage differentiation and gamma interferon (IFN-γ) protein expression by CD4
+
T cells. As CD4
+
Th1 differentiation is associated with negative regulation of CD4
+
Th2 and Th17 differentiation, we hypothesized that RSV infection of STAT4
−/−
mice would result in enhanced lung Th2 and Th17 inflammation and impaired lung Th1 inflammation compared to wild-type (WT) mice. We performed primary and secondary RSV challenges in WT and STAT4
−/−
mice and used STAT1
−/−
mice as a positive control for the development of RSV-specific lung Th2 and Th17 inflammation during primary challenge. Primary RSV challenge of STAT4
−/−
mice resulted in decreased T-bet and IFN-γ expression levels in CD4
+
T cells compared to those of WT mice. Lung Th2 and Th17 inflammation did not develop in primary RSV-challenged STAT4
−/−
mice. Decreased IFN-γ expression by NK cells, CD4
+
T cells, and CD8
+
T cells was associated with attenuated weight loss and enhanced viral clearance with primary challenge in STAT4
−/−
mice compared to WT mice. Following secondary challenge, WT and STAT4
−/−
mice also did not develop lung Th2 or Th17 inflammation. In contrast to primary challenge, secondary RSV challenge of STAT4
−/−
mice resulted in enhanced weight loss, an increased lung IFN-γ expression level, and an increased lung RSV-specific CD8
+
T cell response compared to those of WT mice. These data demonstrate that STAT4 regulates the RSV-specific CD8
+
T cell response to secondary infection but does not independently regulate lung Th2 or Th17 immune responses to RSV challenge.

IMPORTANCE
STAT4 is a protein critical for both innate and adaptive immune responses to viral infection. Our results show that STAT4 regulates the immune response to primary and secondary challenge with RSV but does not restrain RSV-induced lung Th2 or Th17 immune responses. These findings suggest that STAT4 expression may influence lung immunity and severity of illness following primary and secondary RSV infections.
Primary tuberculosis of the palate
Authors: Rosado Pablo , Fuente Eduardo , Gallego Lorena , Calvo Nicolás
Published: June 2014

Tuberculosis (TB) is a life-threatening infectious disease with a high world incidence. However, TB with oral expression is considered rare. The importance of recognising this entity lies in its early diagnosis and treatment, as it can be easily confused with neoplastic or traumatic ulcers. We present a case of a primary TB located in the hard palate and gingiva in an 88-year-old woman.
Aromatase inhibition in relapsing low malignant potential serous tumours of the ovary
Authors: Esfahani Khashayar , Ferrario Cristiano , Le Philippe , Panasci Lawrence
Published: June 2014

Low malignant potential serous tumours (LMPSTs) of the ovary represent an indolent disease, with an excellent prognosis in a majority of patients. Patients with recurrent LMPSTs tend to develop widespread disease with a mortality rate as high as 70%. These tumours tend to have a very poor response to standard chemotherapy, and the management of primary and recurrent disease beyond surgical resection is not well defined. The majority of LMPST have been reported to express oestrogen and progesterone hormone receptors. However, only three reported cases of antihormonal treatment in this setting, and only one using aromatase inhibitors (AI), have been previously reported. We herein report long-term complete remission of two patients with relapsed, chemotherapy-resistant LMPSTs, treated with long-term AI (anastrozole 1 mg daily) as per negative MRI and positron emission tomography scans. Our results warrant further investigation for the use of AIs for metastatic recurrent LMPSTs.
Aphasia due to isolated infarction of the corpus callosum
Authors: Saba Sami , Blum Sonja
Published: June 2014

A 63-year-old man with an isolated infarction of the corpus callosum developed expressive aphasia in addition to the deficits traditionally associated with a disconnection syndrome.
Transrectal impalement of an incense stick in a child presenting as foreign body in the urinary bladder
Authors: Singha Mahapatra Rajkumar , Priyadarshi Vinod , Sarma Madduri Vijay kumar , Pal Dilip Kumar
Published: June 2014

The diversity of objects that can be found in the urinary bladder often surpasses the urologist's imagination and mostly they are introduced per urethrally. Impalement injuries of the rectum with bladder perforation have been rarely reported. A high index of clinical suspicion is required to make the diagnosis of bladder perforation while assessing patients presenting with rectal impalement. In this interesting case, a young male child presented with haematuria and dysuria. He had a history of accidentally sitting on an agarbatti (Indian incense stick) stand while playing, followed by perianal pain which subsided spontaneously. Next day he presented with haematuria and dysuria. Clinical examination was inconclusive. On thorough investigation, a linear echogenic foreign body was found in the urinary bladder. The child was operated and the foreign body (incense stick) was removed. This is the first reported case of rectal impalement injury with incense stick, migrated to the urinary bladder in a 2-year-old child.