bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the AmpliVue, BD Max System, and
illumi
gene Molecular Assays for Detection of Group B Streptococcus in Antenatal Screening Specimens
Authors: Miller Shelley A. , Deak Eszter , Humphries Romney 
Published: March 2015

ABSTRACT

The performances of the AmpliVue, BD Max, and
illumi
gene group B
Streptococcus
(GBS) nucleic acid amplification tests (NAATs) were compared to that of enriched culture for detection of GBS in antenatal screening specimens. Two hundred specimens were tested simultaneously with the NAATs, following 18 to 24 h of Lim broth enrichment; 15% of specimens were culture positive for GBS, whereas 31.5% were positive by at least one NAAT. All three NAATs were more sensitive (sensitivity, 90.9 to 100%) than culture (sensitivity, 53.6%).
Comparison of the Vidas C. difficile GDH Automated Enzyme-Linked Fluorescence Immunoassay (ELFA) with Another Commercial Enzyme Immunoassay (EIA) (Quik Chek-60), Two Selective Media, and a PCR Assay for
gluD
for Detection of Clostridium difficile in Fecal Samples
Authors: Davies K. A. , Berry C. E. , Morris K. A. , Smith R. , Young S. , Davis T. E. , Fuller D. D. , Buckner R. J. , Wilcox M. H. 
Published: March 2015

ABSTRACT

Prevention and management of
Clostridium difficile
infection (CDI) can be improved by rapid and reliable diagnostics. The Vidas
C. difficile
glutamate dehydrogenase assay had performance comparable to that of the Quik Chek-60 assay (overall agreement, 95%) and a sensitivity of >93%; thus, it is suitable as the first test in two-stage algorithms for a CDI diagnosis.
Universal Primers for Detection and Sequencing of Hepatitis B Virus Genomes across Genotypes A to G
Authors: Chook Jack Bee , Teo Woon Li , Ngeow Yun Fong , Tee Kok Keng , Ng Kee Peng , Mohamed Rosmawati 
Published: March 2015

ABSTRACT
Hepatitis B virus (HBV) has been divided into 10 genotypes, A to J, based on an 8% nucleotide sequence divergence between genotypes. The conventional practice of using a single set of primers to amplify a near-complete HBV genome is hampered by its low analytical sensitivity. The current practice of using overlapping conserved primer sets to amplify a complete HBV genome in a clinical sample is limited by the lack of pan-primers to detect all HBV genotypes. In this study, we designed six highly conserved, overlapping primer sets to cover the complete HBV genome. We based our design on the sequences of 5,154 HBV genomes of genotypes A to I downloaded from the GenBank nucleotide database. These primer sets were tested on 126 plasma samples from Malaysia, containing genotypes A to D and with viral loads ranging from 20 to >79,780,000 IU/ml. The overall success rates for PCR amplification and sequencing were >96% and >94%, respectively. Similarly, there was 100% amplification and sequencing success when the primer sets were tested on an HBV reference panel of genotypes A to G. Thus, we have established primer sets that gave a high analytical sensitivity for PCR-based detection of HBV and a high rate of sequencing success for HBV genomes in most of the viral genotypes, if not all, without prior known sequence data for the particular genotype/genome.
Borrelia burgdorferi Not Confirmed in Human-Biting Amblyomma americanum Ticks from the Southeastern United States
Authors: Stromdahl Ellen Y. , Nadolny Robyn M. , Gibbons Jennifer A. , Auckland Lisa D. , Vince Mary A. , Elkins Chad E. , Murphy Michael P. , Hickling Graham J. , Eshoo Mark W. , Carolan Heather E. , Crowder Chris D. , Pilgard Mark A. , Hamer Sarah A. 
Published: March 2015

ABSTRACT

The predominant human-biting tick throughout the southeastern United States is
Amblyomma americanum
. Its ability to transmit pathogens causing Lyme disease-like illnesses is a subject of ongoing controversy. Results of previous testing by the Department of Defense Human Tick Test Kit Program and other laboratories indicated that it is highly unlikely that
A. americanum
transmits any pathogen that causes Lyme disease. In contrast, a recent publication by Clark and colleagues (K. L. Clark, B. Leydet, and S. Hartman, Int. J. Med. Sci. 10:915–931, 2013) reported detection of Lyme group
Borrelia
in
A. americanum
using a nested-flagellin-gene PCR. We evaluated this assay by using it and other assays to test 1,097
A. americanum
ticks collected from humans. Using the Clark assay, in most samples we observed nonspecific amplification and nonrepeatability of results on subsequent testing of samples. Lack of reaction specificity and repeatability is consistent with mispriming, likely due to high primer concentrations and low annealing temperatures in this protocol. In six suspect-positive samples,
Borrelia lonestari
was identified by sequencing of an independent gene region; this is not a Lyme group spirochete and is not considered zoonotic.
B. burgdorferi
was weakly amplified from one pool using some assays, but not others, and attempts to sequence the amplicon of this pool failed, as did attempts to amplify and sequence
B. burgdorferi
from the five individual samples comprising this pool. Therefore,
B. burgdorferi
was not confirmed in any sample. Our results do not support the hypothesis that
A. americanum
ticks are a vector for Lyme group
Borrelia
infections.
Pan-Serotype Diagnostic for Foot-and-Mouth Disease Using the Consensus Antigen of Nonstructural Protein 3B
Authors: Van Dreumel Alyssa K. , Michalski Wojtek P. , McNabb Leanne M. , Shiell Brian J. , Singanallur Nagendrakumar B. , Peck Grantley R. 
Published: March 2015

ABSTRACT
An amino acid consensus sequence for the seven serotypes of foot-and-mouth disease virus (FMDV) nonstructural protein 3B, including all three contiguous repeats, and its use in the development of a pan-serotype diagnostic test for all seven FMDV serotypes are described. The amino acid consensus sequence of the 3B protein was determined from a multiple-sequence alignment of 125 sequences of 3B. The consensus 3B (c3B) protein was expressed as a soluble recombinant fusion protein with maltose-binding protein (MBP) using a bacterial expression system and was affinity purified using amylose resin. The MBP-c3B protein was used as the antigen in the development of a competition enzyme-linked immunosorbent assay (cELISA) for detection of anti-3B antibodies in bovine sera. The comparative diagnostic sensitivity and specificity at 47% inhibition were estimated to be 87.22% and 93.15%, respectively. Reactivity of c3B with bovine sera representing the seven FMDV serotypes demonstrated the pan-serotype diagnostic capability of this bioreagent. The consensus antigen and competition ELISA are described here as candidates for a pan-serotype diagnostic test for FMDV infection.
SLAM- and Nectin-4-Independent Noncytolytic Spread of Canine Distemper Virus in Astrocytes
Authors: Alves Lisa , Khosravi Mojtaba , Avila Mislay , Ader-Ebert Nadine , Bringolf Fanny , Zurbriggen Andreas , Vandevelde Marc , Plattet Philippe 
Published: March 2015

ABSTRACT
Measles and canine distemper viruses (MeV and CDV, respectively) first replicate in lymphatic and epithelial tissues by using SLAM and nectin-4 as entry receptors, respectively. The viruses may also invade the brain to establish persistent infections, triggering fatal complications, such as subacute sclerosis pan-encephalitis (SSPE) in MeV infection or chronic, multiple sclerosis-like, multifocal demyelinating lesions in the case of CDV infection. In both diseases, persistence is mediated by viral nucleocapsids that do not require packaging into particles for infectivity but are directly transmitted from cell to cell (neurons in SSPE or astrocytes in distemper encephalitis), presumably by relying on restricted microfusion events. Indeed, although morphological evidence of fusion remained undetectable, viral fusion machineries and, thus, a putative cellular receptor, were shown to contribute to persistent infections. Here, we first showed that nectin-4-dependent cell-cell fusion in Vero cells, triggered by a demyelinating CDV strain, remained extremely limited, thereby supporting a potential role of nectin-4 in mediating persistent infections in astrocytes. However, nectin-4 could not be detected in either primary cultured astrocytes or the white matter of tissue sections. In addition, a bioengineered “nectin-4-blind” recombinant CDV retained full cell-to-cell transmission efficacy in primary astrocytes. Combined with our previous report demonstrating the absence of SLAM expression in astrocytes, these findings are suggestive for the existence of a hitherto unrecognized third CDV receptor expressed by glial cells that contributes to the induction of noncytolytic cell-to-cell viral transmission in astrocytes.

IMPORTANCE
While persistent measles virus (MeV) infection induces SSPE in humans, persistent canine distemper virus (CDV) infection causes chronic progressive or relapsing demyelination in carnivores. Common to both central nervous system (CNS) infections is that persistence is based on noncytolytic cell-to-cell spread, which, in the case of CDV, was demonstrated to rely on functional membrane fusion machinery complexes. This inferred a mechanism where nucleocapsids are transmitted through macroscopically invisible microfusion events between infected and target cells. Here, we provide evidence that CDV induces such microfusions in a SLAM- and nectin-4-independent manner, thereby strongly suggesting the existence of a third receptor expressed in glial cells (referred to as GliaR). We propose that GliaR governs intercellular transfer of nucleocapsids and hence contributes to viral persistence in the brain and ensuing demyelinating lesions.
Mechanism of HIV-1 Resistance to Short-Peptide Fusion Inhibitors Targeting the Gp41 Pocket
Authors: Su Yang , Chong Huihiui , Qiu Zonglin , Xiong Shengwen , He Yuxian 
Published: March 2015

ABSTRACT
The deep hydrophobic pocket on the N trimer of HIV-1 gp41 has been considered an ideal drug target. On the basis of the M-T hook structure, we recently developed short-peptide-based HIV-1 fusion inhibitors (MTSC22 and HP23), which mainly target the pocket site and possess highly potent antiviral activity. In this study, we focused on investigating their resistance pathways and mechanisms by escape HIV-1 mutants to SC22EK, a template peptide for MTSC22 and HP23. Two substitutions, E49K and N126K, located, respectively, at the N- and C-heptad repeat regions of gp41, were identified as conferring high resistance to the inhibitors targeting the pocket and cross-resistance to enfuvirtide (T20) and sifuvirtide (SFT). The underlying mechanisms of SC22EK-induced resistance include the following: (i) significantly reduced binding affinity of the inhibitors, (ii) dramatically enhanced interaction of the viral six-helix bundle, and (iii)severely damaged functionality of the viral Env complex. Our data have provided important information for the structure-function relationship of gp41 and the structure-activity relationship of viral fusion inhibitors.

IMPORTANCE
Enfuvirtide (T20) is the only HIV-1 fusion inhibitor in clinical use, but the problem of resistance significantly limits its use, calling for new strategies or concepts to develop next-generation drugs. On the basis of the M-T hook structure, short-peptide HIV-1 fusion inhibitors specifically targeting the gp41 pocket site exhibit high binding and antiviral activities. Here, we investigated the molecular pathway of HIV-1 resistance to the short inhibitors by selecting and mapping the escape mutants. The key substitutions for resistance and the underlying mechanisms have been finely characterized. The data provide important information for the structure-function relationship of gp41 and its inhibitors and will definitely help our future development of novel drugs that block gp41-dependent fusion.
Highly Divergent Hepaciviruses from African Cattle
Authors: Corman Victor Max , Grundhoff Adam , Baechlein Christine , Fischer Nicole , Gmyl Anatoly , Wollny Robert , Dei Dickson , Ritz Daniel , Binger Tabea , Adankwah Ernest , Marfo Kwadwo Sarfo , Annison Lawrence , Annan Augustina , Adu-Sarkodie Yaw , Oppong Samuel , Becher Paul , Drosten Christian , Drexler Jan Felix 
Published: March 2015

ABSTRACT

The hepatitis C virus (HCV; genus
Hepacivirus
) is a highly relevant human pathogen. Unique hepaciviruses (HV) were discovered recently in animal hosts. The direct ancestor of HCV has not been found, but the genetically most closely related animal HVs exist in horses. To investigate whether other peridomestic animals also carry HVs, we analyzed sera from Ghanaian cattle for HVs by reverse transcription-PCR (RT-PCR). Nine of 106 specimens from different sampling sites contained HV RNA (8.5%) at median viral loads of 1.6 × 10
5
copies/ml. Infection seemed unrelated to cattle age and gender. Near-full-genome sequencing of five representative viruses confirmed taxonomic classifications. Cattle HVs formed two distinct phylogenetic lineages that differed by up to 17.7% on the nucleotide level in the polyprotein-encoding region, suggesting cocirculation of different virus subtypes. A conserved microRNA122-binding site in the 5′ internal ribosomal entry site suggested liver tropism of cattle HVs. Phylogenetic analyses suggested the circulation of HVs in cattle for several centuries. Cattle HVs were genetically highly divergent from all other HVs, including HCV. HVs from genetically related equine and bovine hosts were not monophyletic, corroborating host shifts during the evolution of the genus
Hepacivirus
. Similar to equine HVs, the genetic diversity of cattle HVs was low compared to that of HCV genotypes. This suggests an influence of the human-modified ecology of peridomestic animals on virus diversity. Further studies should investigate the occurrence of cattle HVs in other geographic areas and breeds, virus pathogenicity in cattle, and the potential exposure of human risk groups, such as farmers, butchers, and abattoir workers.

IMPORTANCE
HCV (genus
Hepacivirus
) is a major human pathogen, causing liver failure and cancer. Unique hepaciviruses (HVs) were discovered over the last few years in animals, but the direct ancestor of HCV has not been found. The animal HV most closely related to HCV so far originated from horses, suggesting that other livestock animals also harbor HVs. Therefore, we investigated African cattle and discovered previously unknown HVs at high prevalence and viral loads. Because of the agricultural importance of cattle, it may be relevant to investigate HV pathogenicity. The frequent exposure of humans to cattle also may warrant investigations of the zoonotic potential of these viruses. Evolutionary analyses suggested that cattle HVs have existed for centuries. Despite the genetic relatedness of their animal hosts, HVs from cattle and horses were not phylogenetically related, corroborating frequent host shifts during the evolution of the genus
Hepacivirus
.
Aharonov–Bohm effect revisited
Authors: Eskin Gregory 
Published: March 2015

Aharonov–Bohm effect is a quantum mechanical phenomenon that attracted the attention of many physicists and mathematicians since the publication of the seminal paper of Aharonov and Bohm [1] in 1959.We consider different types of Aharonov–Bohm effects such as the magnetic AB effect, electric AB effect, combined electromagnetic AB effect, AB effect for the Schrödinger equations with Yang–Mills potentials, and the gravitational analog of AB effect.We shall describe different approaches to prove the AB effect based on the inverse scattering problems, the inverse boundary value problems in the presence of obstacles, spectral asymptotics, and the direct proofs of the AB effect.
26th Pezcoller Symposium: Cancers Driven by Hormones
Authors: Brown Myles , Chinnaiyan Arul , Farsetti Antonella , Livingston David M. , Loda Massimo , Schuele Roland , Mihich Enrico 
Published: March 2015

Abstract
This symposium was held in Trento, Italy, on June 19–21, 2014, and was focused on advances in biology, physiology, and pathology of neoplasms affected by hormones, especially breast and prostate cancers. The stem cell function, the genetic and epigenetic interactions with hormones, the mechanisms of estrogen receptor transcription, biochemical markers and therapeutic targets in breast cancer, promotion of breast cancer carcinogenesis by progesterone, the basis for prostate cancer progression and the relevance of DNA repair processes, androgen receptor programming during prostate carcinogenesis, the metabolic stress role in tumor survival, and the diagnostic use of imaging in prostate cancer were discussed. Cancer Res; 75(7); 1177–80. ©2015 AACR.
A Chemical Genetics Approach for the Functional Assessment of Novel Cancer Genes
Authors: Zhou Qianhe , Derti Adnan , Ruddy David , Rakiec Daniel , Kao Iris , Lira Michelle , Gibaja Veronica , Chan HoMan , Yang Yi , Min Junxia , Schlabach Michael R. , Stegmeier Frank 
Published: March 2015

Abstract
Assessing the functional significance of novel putative oncogenes remains a significant challenge given the limitations of current loss-of-function tools. Here, we describe a method that employs TALEN or CRISPR/Cas9-mediated knock-in of inducible degron tags (Degron-KI) that provides a versatile approach for the functional characterization of novel cancer genes and addresses many of the shortcomings of current tools. The Degron-KI system allows for highly specific, inducible, and allele-targeted inhibition of endogenous protein function, and the ability to titrate protein depletion with this system is able to better mimic pharmacologic inhibition compared with RNAi or genetic knockout approaches. The Degron-KI system was able to faithfully recapitulate the effects of pharmacologic EZH2 and PI3Kα inhibitors in cancer cell lines. The application of this system to the study of a poorly understood putative oncogene, SF3B1, provided the first causal link between SF3B1 hotspot mutations and splicing alterations. Surprisingly, we found that SF3B1-mutant cells are not dependent upon the mutated allele for in vitro growth, but instead depend upon the function of the remaining wild-type alleles. Collectively, these results demonstrate the broad utility of the Degron-KI system for the functional characterization of cancer genes. Cancer Res; 75(10); 1949–58. ©2015 AACR.
Endostatin Has ATPase Activity, Which Mediates Its Antiangiogenic and Antitumor Activities
Authors: Wang Shan , Lu Xin-an , Liu Peng , Fu Yan , Jia Lin , Zhan Shunli , Luo Yongzhang 
Published: March 2015

Abstract
Endostatin is an endogenous angiogenesis inhibitor with broad-spectrum antitumor activities. Although the molecular mechanisms of endostatin have been extensively explored, the intrinsic biochemical characteristics of endostatin are not completely understood. Here, we revealed for the first time that endostatin embedded novel ATPase activity. Moreover, mutagenesis study showed that the ATPase activity of endostatin mutants positively correlated with effects on endothelial cell activities and tumor growth. E-M, an endostatin mutant with higher ATPase activity than that of wild-type (WT) endostatin, significantly increased endostatin-mediated inhibitory effects on endothelial cell proliferation, migration, tube formation, and adhesion. In vivo study showed that E-M displayed enhanced antitumor effects compared with WT. On the other hand, K96A, K96R, and E176A, endostatin mutants with lower ATPase activities than that of WT, showed reduced or comparable effects on targeting both in vitro endothelial cell activities and in vivo tumor angiogenesis and tumor growth. Furthermore, endostatin and its mutants exhibited distinct abilities in regulations of gene expression (Id1, Id3), cell signaling (Erk, p38, and Src phosphorylation), and intracellular ATP levels. Collectively, our study demonstrates that endostatin has novel ATPase activity, which mediates its antiangiogenic and antitumor activities, suggesting that construction of endostatin analogues with high ATPase activity may provide a new direction for the development of more potent antiangiogenic drugs. Mol Cancer Ther; 14(5); 1192–201. ©2015 AACR.
Titrating haemophilia B phenotypes using siRNA strategy: evidence that antithrombotic activity is separated from bleeding liability
Authors: Thankappan Anil , R. Strapps Walter , DiPietro Marti , Leander Karen , Zhang Zuo , K. Shin Myung , Levorse John , Desai Kunal , Xu Yiming , Lai KehDih , Wu Weizhen , Chen Zhu , Cai Tian-Quan , Jochnowitz Nina , Bentley Ross , Hoos Lizbeth , Zhou Yuchen , Sepp-Lorenzino Laura , Seiffert Dietmar , M. Metzger Joseph , Tadin-Strapps Marija , Andre Patrick 
Published: March 2015

SummaryHaemophilia A and B are characterised by a life-long bleeding predisposition, and several lines of evidence suggest that risks of atherothrombotic events may also be reduced. Establishing a direct correlation between coagulation factor levels, thrombotic risks and bleeding propensity has long been hampered by an inability to selectively and specifically inhibit coagulation factor levels. Here, the exquisite selectivity of gene silencing combined with a gene knockout (KO) approach was used to define the relative contribution of factor IX (fIX) to thrombosis and primary haemostasis in the rat. Using a lipid nanoparticle (LNP) formulation, we successfully delivered fIX siRNAs to the liver by intravenous administration. The knockdown (KD) of target gene mRNA was achieved rapidly (within 24 hour post-siRNA dosing), sustained (maintained for at least 7 days post dosing) and not associated with changes in mRNA expression levels of other coagulation factors. We found that intermediate levels of liver fIX mRNA silencing (60–95 %) translating into a 50–99 % reduction of plasma fIX activity provided protection from thrombosis without prolonging the cuticle bleeding time. Over 99 % inhibition of fIX activity was required to observe increase in bleeding, a phenotype confirmed in fIX KO rats. These data provide substantial evidence of a participation of fIX in the mechanisms regulating thrombosis prior to those regulating primary haemostasis, therefore highlighting the potential of fIX as a therapeutic target. In addition, hepatic mRNA silencing using LNP-encapsulated siRNAs may represent a promising novel approach for the chronic treatment and prevention of coagulation-dependent thrombotic disorders in humans.
Zinc delays clot lysis by attenuating plasminogen activation and plasmin-mediated fibrin degradation
Authors: Henderson Sara J. , Stafford Alan R. , Leslie Beverly A. , Kim Paul Y. , Vaezzadeh Nima , Ni Ran , Fredenburgh James C. , Weitz Jeffrey I. 
Published: March 2015

SummaryZinc circulates free in plasma at a concentration of 0.1–2 μM, but its levels increase locally when it is released from activated platelets. Although zinc influences many processes in haemostasis, its effect on fibrinolysis has not been thoroughly investigated. Using a fluorescent zinc-binding probe, we demonstrated that zinc binds tissue-type plasminogen activator (tPA) and plasmin with high affinity (Kd values of 0.2 μM), and surface plasmon resonance studies revealed that zinc binds fibrin with a Kd of 12.8 μM. Zinc had no effect on the affinity of plasminogen or plasmin for fibrin, but increased the affinity of tPA by two-fold. In the presence of 5 μM zinc, the catalytic efficiency of plasminogen activation by tPA was reduced by approximately two-fold, both in the absence or presence of fibrin. Zinc attenuated plasminmediated degradation of the fibrinogen alpha-chain by 43 %, but had no effect on trypsin degradation. tPA-mediated fibrin clot lysis was prolonged 2.5-fold by zinc in a concentration-dependent fashion, and tPA-mediated plasma clot lysis was attenuated by 1.5-fold. Therefore, our data indicate that zinc modulates fibrinolysis by attenuating tPAmediated plasminogen activation and plasmin-induced fibrin degradation. These findings suggest that local release of zinc by platelets attenuates fibrinolysis.