bluuebunny/crossref_metadata_2025_split huggingface dataset:
The special linear version of the projective bundle theorem
Authors: Ananyevskiy Alexey 
Published: November 2014

AbstractA special linear Grassmann variety$\text{SGr}(k,n)$is the complement to the zero section of the determinant of the tautological vector bundle over$\text{Gr}(k,n)$. For an$SL$-oriented representable ring cohomology theory$A^{\ast }(-)$with invertible stable Hopf map${\it\eta}$, including Witt groups and$\text{MSL}_{{\it\eta}}^{\ast ,\ast }$, we have$A^{\ast }(\text{SGr}(2,2n+1))\cong A^{\ast }(pt)[e]/(e^{2n})$, and$A^{\ast }(\text{SGr}(k,n))$is a truncated polynomial algebra over$A^{\ast }(pt)$whenever$k(n-k)$is even. A splitting principle for such theories is established. Using the computations for the special linear Grassmann varieties, we obtain a description of$A^{\ast }(\text{BSL}_{n})$in terms of homogeneous power series in certain characteristic classes of tautological bundles.
Differentiation of Classical Swine Fever Virus Infection from CP7_E2alf Marker Vaccination by a Multiplex Microsphere Immunoassay
Authors: Xia Hongyan , Harimoorthy Rajiv , Vijayaraghavan Balaje , Blome Sandra , Widén Frederik , Beer Martin , Belák Sándor , Liu Lihong 
Published: November 2014

ABSTRACTClassical swine fever (CSF) is a highly contagious viral disease of pigs that has a tremendous socioeconomic impact. Vaccines are available for disease control. However, most industrialized countries are implementing stamping-out strategies to eliminate the disease and avoid trade restrictions. These restrictions can be avoided through the use of marker vaccines such as CP7_E2alf. Marker vaccines have to be accompanied by reliable and robust discriminatory assays. In this context, a multiplex microsphere immunoassay for serological differentiation of infected from vaccinated animals (DIVA) was developed to distinguish CSF virus (CSFV)-infected animals from CP7_E2alf-vaccinated animals. To this end, three viral proteins, namely, CSFV E2, CSFV Erns, and bovine viral diarrhea virus (BVDV) E2, were produced in insect cells using a baculovirus expression system; they were used as antigens in a microsphere immunoassay, which was further evaluated by testing a large panel of pig sera and compared to a well-characterized commercial CSFV E2 antibody enzyme-linked immunosorbent assays (ELISAs) and a test version of an improved CSFV Ernsantibody ELISA. Under a cutoff median fluorescence intensity value of 5,522, the multiplex microsphere immunoassay had a sensitivity of 98.5% and a specificity of 98.9% for the detection of antibodies against CSFV E2. The microsphere immunoassay and the CSFV ErnsELISA gave the same results for 155 out of 187 samples (82.8%) for the presence of CSFV Ernsantibodies. This novel multiplex immunoassay is a valuable tool for measuring and differentiating immune responses to vaccination and/or infection in animals.
Draft Genome Sequence of Chromobacterium haemolyticum Causing Human Bacteremia Infection in Japan
Authors: Miki Tsuyoshi , Okada Nobuhiko 
Published: November 2014

ABSTRACT

Chromobacterium haemolyticum
is a Gram-negative bacterium displaying remarkable hemolysis against human and sheep erythrocytes. In addition,
C. haemolyticum
infects humans, in which the infection mechanism remains unknown. We report here the draft genome sequence of
C. haemolyticum
strain T124, isolated from a young patient with sepsis in Japan.
Complete Genome Assembly of Staphylococcus epidermidis AmMS 205
Authors: Davenport K. W. , Daligault H. E. , Minogue T. D. , Bishop-Lilly K. A. , Broomall S. M. , Bruce D. C. , Chain P. S. , Coyne S. R. , Frey K. G. , Gibbons H. S. , Jaissle J. , Redden C. L. , Rosenzweig C. N. , Scholz M. B. , Teshima H. , Johnson S. L. 
Published: November 2014

ABSTRACT

Staphylococcus epidermidis
causes a large number of catheter-related sepsis infections annually in the United States. We present the 2.54-Mbp complete genome assembly of reference strain
S. epidermidis
AmMS 205, including a single 37.7-kbp plasmid. The annotated assembly is available in GenBank under accession numbers CP009046 and CP009047.
Draft Genome Sequence of Non-O1 and Non-O139 Vibrio cholerae Strain VCC19
Authors: de Sá Pablo Caracciolo Gomes , Da Silva Miriam Lopes , Carneiro Adriana Ribeiro , Gomes Jaqueline Conceição Meireles , Dias Larissa Maranhão , Alves Jorianne Thyeska Castro , De Oliveira Veras Adonney Allan , Baraúna Rafael Azevedo , Das Graças Diego Assis , Matté Maria Helena , Sato Maria Ines Zanolli , Hachich Elayse Maria , Matté Glavur Rogério , Ramos Rommel Thiago Jucá , Silva Artur 
Published: November 2014

ABSTRACT

Vibrio cholerae
O1 is the causative agent of cholera and is ubiquitous in the aquatic environment, while
V. cholerae
strains non-O1 and non-O139 are recognized as causative agents of sporadic and localized outbreaks of diarrhea. Here, we report the complete sequence of a non-O1 and non-O139
V. cholerae
strain (VCC19), which was isolated from the environment in Brazil. The sequence includes the integrative conjugative element (ICE). This paper is the first report of the presence of such an element in a
V. cholerae
strain isolated in Brazil.
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp.
aureus
ATCC 25923
Authors: Treangen Todd J. , Maybank Rosslyn A. , Enke Sana , Friss Mary Beth , Diviak Lynn F. , Karaolis David K. R. , Koren Sergey , Ondov Brian , Phillippy Adam M. , Bergman Nicholas H. , Rosovitz M. J. 
Published: November 2014

ABSTRACT

Staphylococcus aureus
subsp.
aureus
ATCC 25923 is commonly used as a control strain for susceptibility testing to antibiotics and as a quality control strain for commercial products. We present the completed genome sequence for the strain, consisting of the chromosome and a 27.5-kb plasmid.
Draft Genome Sequence of
Sulfitobacter
sp. CB2047, a Member of the
Roseobacter
Clade of Marine Bacteria, Isolated from an
Emiliania huxleyi
Bloom
Authors: Ankrah Nana Y. D. , Lane Thomas , Budinoff Charles R. , Hadden Mary K. , Buchan Alison 
Published: November 2014

ABSTRACT

We announce the draft genome sequence of
Sulfitobacter
sp. strain CB2047, a marine bacterium of the
Roseobacter
clade, isolated from a phytoplankton bloom. The genome encodes pathways for the catabolism of aromatic compounds as well as transformations of carbon monoxide and sulfur species. The strain also encodes a prophage as well as the gene transfer agent (GTA), both of which are prevalent among members of the
Rhodobacterales
order.
Draft Genome Sequence of Bacillus fengqiuensis FJAT-14578, Isolated from a Soil Sample in China
Authors: Liu Guo-Hong , Liu Bo , Tang Jian-Yang , Che Jian-Mei , Zhu Yu-Jing , Su Ming-Xing , Wang Jie-Ping , Chen Qian-Qian 
Published: November 2014

ABSTRACT

Here, we report the first high-quality draft genome sequence of
Bacillus fengqiuensis
FJAT-14578, isolated from a soil sample collected from China. The genome size was 5,569,389 bp, with a 40.93 mol% G+C content. The number of tRNAs was 69 and of rRNAs was 10 (5S, 16S, and 23S).
Whole-Genome Sequences of Five Oligotrophic Bacteria Isolated from Deep within Lechuguilla Cave, New Mexico
Authors: Gan Huan You , Gan Han Ming , Tarasco Alexander Mario , Busairi Nurfatini Idayu , Barton Hazel A. , Hudson André O. , Savka Michael A. 
Published: November 2014

ABSTRACT

Here, we report the whole-genome sequences and annotation of five oligotrophic bacteria from two sites within the Lechuguilla Cave in the Carlsbad Caverns National Park, NM. Three of the five genomes contain an acyl-homoserine lactone signal synthase ortholog (
luxI
) that is involved in cell-to-cell communication via quorum sensing.
Draft Genome Sequence of a Novel SAR11 Clade Species Abundant in a Tibetan Lake
Authors: Oh Seungdae , Zhang Rui , Wu Qinglong L. , Liu Wen-Tso 
Published: November 2014

ABSTRACT
SAR11 clade bacteria are abundant and play a key role in the nutrient cycles of marine and, presumably, inland aquatic environments. We report here the draft genome sequence of a novel species in the SAR11 cluster, reconstructed from a metagenomic data set obtained from a Tibetan lake.
Draft Genome Sequence of Bacillus subtilis Strain NKYL29, an Antimicrobial-Peptide-Producing Strain from Soil
Authors: Jiang Yanbin , Xu Haijin , Li Ying , Liu Hongbin , Yu Lei , Qiao Mingqiang , Liu Gang 
Published: November 2014

ABSTRACT

Bacillus subtilis
strain NKYL29 is an antimicrobial-peptide-producing strain isolated from the soil of Ranzhuang Tunnel in Hebei Province, China. Here, we present the draft genome of this strain, which provides the genetic basis for application of the antimicrobial peptide.
Draft Genome Sequence of the Iron-Oxidizing Acidophile Leptospirillum ferriphilum Type Strain DSM 14647
Authors: Cárdenas Juan Pablo , Lazcano Marcelo , Ossandon Francisco J. , Corbett Melissa , Holmes David S. , Watkin Elizabeth 
Published: November 2014

ABSTRACT

The genomic features of the
Leptospirillum ferriphilum
type strain DSM 14647 are described here. An analysis of the predicted genes enriches our knowledge of the molecular basis of iron oxidation, improves our understanding of its role in industrial bioleaching, and suggests how it is adapted to live at extremely low pH.
Genome Sequence of Rickettsia hoogstraalii, a Geographically Widely Distributed Tick-Associated Bacterium
Authors: Sentausa Erwin , El Karkouri Khalid , Nguyen Thi-Tien , Caputo Aurélia , Raoult Didier , Fournier Pierre-Edouard 
Published: November 2014

ABSTRACT

Rickettsia hoogstraalii
is a tick-associated member of the spotted fever group rickettsiae that is geographically widely distributed. We report here the draft genome of
R. hoogstraalii
strain Croatica
T
(=DSM 22243 = UTMB 00003), which was isolated from
Haemaphysalis sulcata
ticks collected in Croatia.
Streamlining HIV Testing for HIV Preexposure Prophylaxis
Authors: Guanira Juan V. , Leigler Teri , Kallas Esper , Schechter Mauro , Sharma Usha , Glidden David , Grant Robert M. 
Published: November 2014

ABSTRACT
HIV-testing algorithms for preexposure prophylaxis (PrEP) should be optimized to minimize the risk of drug resistance, the time off PrEP required to evaluate false-positive screening results, and costs and to expedite the start of therapy for those confirmed to be infected. HIV rapid tests (RTs) for anti-HIV antibodies provide results in less than 1 h and can be conducted by nonlicensed staff at the point of care. In many regions, Western blot (WB) testing is required to confirm reactive RT results. WB testing, however, causes delays in diagnosis and adds expense. The iPrEx study evaluated the safety and efficacy of daily oral emtricitabine-tenofovir disoproxil fumarate among HIV-seronegative men and transgender women who have sex with men: HIV infection was assessed with two RTs plus WB confirmation, followed by HIV-1 plasma viral load testing. During the iPrEx study, there were 51,260 HIV status evaluations among 2,499 volunteers using RTs: 142 (0.28%) had concordant positive results (100% were eventually confirmed) and 19 (0.04%) had discordant results among 14 participants; 11 were eventually determined to be HIV infected. A streamlined approach using only one RT to screen and a second RT to confirm (without WB) would have had nearly the same accuracy. Discrepant RT results are best evaluated with nucleic acid testing, which would also increase sensitivity.
Cognate CD4 T-Cell Licensing of Dendritic Cells Heralds Anti-Cytomegalovirus CD8 T-Cell Immunity after Human Allogeneic Umbilical Cord Blood Transplantation
Authors: Flinsenberg T. W. H. , Spel L. , Jansen M. , Koning D. , de Haar C. , Plantinga M. , Scholman R. , van Loenen M. M. , Nierkens S. , Boon L. , van Baarle D. , Heemskerk M. H. M. , Boelens J. J. , Boes M. 
Published: November 2014

ABSTRACT

Reactivation of human cytomegalovirus (CMV) is hazardous to patients undergoing allogeneic cord blood transplantation (CBT), lowering survival rates by approximately 25%. While antiviral treatment ameliorates viremia, complete viral control requires CD8
+
T-cell-driven immunity. Mouse studies suggest that cognate antigen-specific CD4
+
T-cell licensing of dendritic cells (DCs) is required to generate effective CD8
+
T-cell responses. For humans, this was not fully understood. We here show that CD4
+
T cells are essential for licensing of human DCs to generate effector and memory CD8
+
T-cell immunity against CMV in CBT patients. First, we show in CBT recipients that clonal expansion of CMV-pp65-specific CD4
+
T cells precedes the rise in CMV-pp65-specific CD8
+
T cells. Second, the elicitation of CMV-pp65-specific CD8
+
T cells from rare naive precursors in cord blood requires DC licensing by cognate CMV-pp65-specific CD4
+
T cells. Finally, also CD8
+
T-cell memory responses require CD4
+
T-cell-mediated licensing of DCs in our system, by secretion of gamma interferon (IFN-γ) by pp65-specific CD4
+
T cells. Together, these data show that human DCs require licensing by cognate antigen-specific CD4
+
T cells to elicit effective CD8
+
T-cell-mediated immunity and fight off viral reactivation in CBT patients.

IMPORTANCE
Survival rates after stem cell transplantation are lowered by 25% when patients undergo reactivation of cytomegalovirus (CMV) that they harbor. Immune protection against CMV is mostly executed by white blood cells called killer T cells. We here show that for generation of optimally protective killer T-cell responses that respond to CMV, the early elicitation of help from a second branch of CMV-directed T cells, called helper T cells, is required.
The Influenza Virus Neuraminidase Protein Transmembrane and Head Domains Have Coevolved
Authors: da Silva Diogo V. , Nordholm Johan , Dou Dan , Wang Hao , Rossman Jeremy S. , Daniels Robert 
Published: November 2014

ABSTRACT
Transmembrane domains (TMDs) from single-spanning membrane proteins are commonly viewed as membrane anchors for functional domains. Influenza virus neuraminidase (NA) exemplifies this concept, as it retains enzymatic function upon proteolytic release from the membrane. However, the subtype 1 NA TMDs have become increasingly more polar in human strains since 1918, which suggests that selection pressure exists on this domain. Here, we investigated the N1 TMD-head domain relationship by exchanging a prototypical “old” TMD (1933) with a “recent” (2009), more polar TMD and an engineered hydrophobic TMD. Each exchange altered the TMD association, decreased the NA folding efficiency, and significantly reduced viral budding and replication at 37°C compared to at 33°C, at which NA folds more efficiently. Passaging the chimera viruses at 37°C restored the NA folding efficiency, viral budding, and infectivity by selecting for NA TMD mutations that correspond with their polar or hydrophobic assembly properties. These results demonstrate that single-spanning membrane protein TMDs can influence distal domain folding, as well as membrane-related processes, and suggest the NA TMD in H1N1 viruses has become more polar to maintain compatibility with the evolving enzymatic head domain.

IMPORTANCE
The neuraminidase (NA) protein from influenza A viruses (IAVs) functions to promote viral release and is one of the major surface antigens. The receptor-destroying activity in NA resides in the distal head domain that is linked to the viral membrane by an N-terminal hydrophobic transmembrane domain (TMD). Over the last century, the subtype 1 NA TMDs (N1) in human H1N1 viruses have become increasingly more polar, and the head domains have changed to alter their antigenicity. Here, we provide the first evidence that an “old” N1 head domain from 1933 is incompatible with a “recent” (2009), more polar N1 TMD sequence and that, during viral replication, the head domain drives the selection of TMD mutations. These mutations modify the intrinsic TMD assembly to restore the head domain folding compatibility and the resultant budding deficiency. This likely explains why the N1 TMDs have become more polar and suggests the N1 TMD and head domain have coevolved.
Expression of the Epidermodysplasia Verruciformis-Associated Genes
EVER1
and
EVER2
Is Activated by Exogenous DNA and Inhibited by LMP1 Oncoprotein from Epstein-Barr Virus
Authors: Frecha Cecilia , Chevalier Sébastien A. , van Uden Patrick , Rubio Ivonne , Siouda Maha , Saidj Djamel , Cohen Camille , Lomonte Patrick , Accardi Rosita , Tommasino Massimo 
Published: November 2014

ABSTRACT

EVER1
and
EVER2
are mutated in epidermodysplasia verruciformis patients, who are susceptible to human betapapillomavirus (HPV) infection. It is unknown whether their products control the infection of other viruses. Here, we show that the expression of both genes in B cells is activated immediately after Epstein-Barr virus (EBV) infection, whereas at later stages, it is strongly repressed via activation of the NF-κB signaling pathway by latent membrane protein 1 (LMP1). Ectopic expression of
EVER1
impairs the ability of EBV to infect B cells.
Peri- and Postharvest Factors in the Control of Shiga Toxin-Producing
Escherichia coli
in Beef
Authors: Moxley Rodney A. , Acuff Gary R. 
Published: November 2014

ABSTRACT

Certain Shiga toxin-producing
Escherichia coli
(STEC) strains are important causes of food-borne disease, with hemorrhagic colitis and, in some cases, hemolytic-uremic syndrome as the clinical manifestations of illness. Six serogroups and one serotype of STEC (O26, O45, O103, O111, O121, O145, and O157:H7) are responsible for the vast majority of cases in the United States. Based on recent data for all food commodities combined, 55.3% and 50.0% of the outbreaks of STEC O157 and non-O157 in the United States, respectively, are attributable to beef as a food source. Consequently, the U.S. Department of Agriculture, Food Safety and Inspection Service declared these organisms as adulterants in raw, nonintact beef. In North America, cattle are a major reservoir of STEC strains, with organisms shed in the feces and contaminated hides of the animals being the main vehicle for spread to carcasses at slaughter. A number of peri- and postharvest interventions targeting STEC have been developed, and significant progress has been made in improving the microbiological quality of beef in the past 20 years as a result. However, continued improvements are needed, and accurate assessment of these interventions, especially for non-O157 STEC, would greatly benefit from improvements in detection methods for these organisms.
The Serine Recombinases
Authors: Stark W. Marshall 
Published: November 2014

ABSTRACTIn site-specific recombination, two short DNA sequences (‘sites’) are each cut at specific points in both strands, and the cut ends are rejoined to new partners. The enzymes that mediate recognition of the sites and the subsequent cutting and rejoining steps are called recombinases. Most recombinases fall into one of two families according to similarities of their protein sequences and mechanisms; these families are known as the tyrosine recombinases and the serine recombinases, the names referring to the conserved amino acid residue that attacks the DNA phosphodiester and becomes covalently linked to a DNA strand end during catalysis. This chapter gives an overview of our current understanding of the serine recombinases, their types, biological roles, structures, catalytic mechanisms, mechanisms of regulation, and applications.
Plasmid-Mediated Tolerance Toward Environmental Pollutants
Authors: Segura Ana , Molina Lázaro , Ramos Juan Luis 
Published: November 2014

ABSTRACT
The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.
Plasmid Biopharmaceuticals
Authors: Prazeres Duarte Miguel F. , Monteiro Gabriel A. 
Published: November 2014

ABSTRACTPlasmids are currently an indispensable molecular tool in life science research and a central asset for the modern biotechnology industry, supporting its mission to produce pharmaceutical proteins, antibodies, vaccines, industrial enzymes, and molecular diagnostics, to name a few key products. Furthermore, plasmids have gradually stepped up in the past 20 years as useful biopharmaceuticals in the context of gene therapy and DNA vaccination interventions. This review provides a concise coverage of the scientific progress that has been made since the emergence of what are called today plasmid biopharmaceuticals. The most relevant topics are discussed to provide researchers with an updated overview of the field. A brief outline of the initial breakthroughs and innovations is followed by a discussion of the motivation behind the medical uses of plasmids in the context of therapeutic and prophylactic interventions. The molecular characteristics and rationale underlying the design of plasmid vectors as gene transfer agents are described and a description of the most important methods used to deliver plasmid biopharmaceuticalsin vivo(gene gun, electroporation, cationic lipids and polymers, and micro- and nanoparticles) is provided. The major safety issues (integration and autoimmunity) surrounding the use of plasmid biopharmaceuticals is discussed next. Aspects related to the large-scale manufacturing are also covered, and reference is made to the plasmid products that have received marketing authorization as of today.
Fruit and vegetable intake and risk of type 2 diabetes mellitus: meta-analysis of prospective cohort studies
Authors: Li Min , Fan Yingli , Zhang Xiaowei , Hou Wenshang , Tang Zhenyu 
Published: November 2014

ObjectiveTo clarify and quantify the potential dose–response association between the intake of fruit and vegetables and risk of type 2 diabetes.DesignMeta-analysis and systematic review of prospective cohort studies.Data sourceStudies published before February 2014 identified through electronic searches using PubMed and Embase.Eligibility criteria for selecting studiesProspective cohort studies with relative risks and 95% CIs for type 2 diabetes according to the intake of fruit, vegetables, or fruit and vegetables.ResultsA total of 10 articles including 13 comparisons with 24 013 cases of type 2 diabetes and 434 342 participants were included in the meta-analysis. Evidence of curve linear associations was seen between fruit and green leafy vegetables consumption and risk of type 2 diabetes (p=0.059 and p=0.036 for non-linearity, respectively). The summary relative risk of type 2 diabetes for an increase of 1 serving fruit consumed/day was 0.93 (95% CI 0.88 to 0.99) without heterogeneity among studies (p=0.477, I2=0%). For vegetables, the combined relative risk of type 2 diabetes for an increase of 1 serving consumed/day was 0.90 (95% CI 0.80 to 1.01) with moderate heterogeneity among studies (p=0.002, I2=66.5%). For green leafy vegetables, the summary relative risk of type 2 diabetes for an increase of 0.2 serving consumed/day was 0.87 (95% CI 0.81 to 0.93) without heterogeneity among studies (p=0.496, I2=0%). The combined estimates showed no significant benefits of increasing the consumption of fruit and vegetables combined.ConclusionsHigher fruit or green leafy vegetables intake is associated with a significantly reduced risk of type 2 diabetes.