bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breast density measurements with ultrasound tomography: A comparison with film and digital mammography
Authors: Duric Neb , Boyd Norman , Littrup Peter , Sak Mark , Myc Lukasz , Li Cuiping , West Erik , Minkin Sal , Martin Lisa , Yaffe Martin , Schmidt Steven , Faiz Muhammad , Shen Jason , Melnichouk Olga , Li Qing , Albrecht Teri 
Published: January 2013

Purpose:To investigate the use of the whole‐breast sound speed measurement as a marker of breast density (BD), a known risk factor for breast cancer.Methods:As part of an ongoing study of breast cancer detection, 249 patients were scanned with a clinical prototype that operates on the principles of ultrasound tomography. Typically, 40–100 sound speed tomograms were reconstructed from the scan data, corresponding to the entire volume of the breast of each patient. The data were used to estimate the volume averaged sound speed (VASS) of the breast for each patient. The corresponding mammograms were used to calculate mammographic percent density (MPD) usingCUMULUS software. Film mammograms were available for 164 patients while 85 digital mammograms were available for the remaining patients. Standard statistical techniques were used to determine associations of breast sound speed with a variety of mammographic measures such as percent density, area of dense tissue, and area of nondense tissue. Furthermore, associations of breast sound speed with continuous variables such as age and weight and dichotomous variables such as parity and menopausal status were also assessed.Results:VASS was found to be significantly associated with MPD. The Spearman correlation coefficient (rs) between VASS and MPD was found to be 0.77 and 0.71 for film and digital mammography, respectively. VASS was positively correlated with dense areas by mammography, both digital (rs = 0.46) and film (rs = 0.56). VASS was negatively associated with nondense area by mammography, both digital (rs = −0.58) and film (rs = −0.63). BD by all methods was less in postmenopausal than in premenopausal women. The MPD was lower in the postmenopausal group (by 6.6%, p < 0.08, for the digital group and 7.73%, p < 0.007, for the film group). The VASS was also lower in the postmenopausal group (by 15 m/s, p < 0.001 for the digital group and 8 m/s, p < 0.08, for the film group). The association of MPD with age was characterized with rs = −0.06 (p < 0.6) for digital mammography and rs = −0.53 (p < 0.002) for film mammography. For weight, the MPD associations were characterized by rs = −0.53 (p < 0.0001) for digital mammography and −0.38 (p < 0.0001) for film mammography. The association of VASS with age was rs = −0.33 (p < 0.002) for the digital group and −0.17 (p < 0.03) for the film group. For weight, the relationship was characterized with rs = −0.45 (p < 0.001) for the digital group and −0.37 (p < 0.0001) for the film group.Conclusions:The association between VASS and MPD is strong for both film and digital mammography, suggesting that VASS is a viable measure of breast density. This result sets the stage for future work that will focus on directly testing the association of VASS with breast cancer risk.
Genetic Characterization of Toxoplasma gondii Revealed Highly Diverse Genotypes for Isolates from Newborns with Congenital Toxoplasmosis in Southeastern Brazil
Authors: Carneiro Ana Carolina Aguiar Vasconcelos , Andrade Gláucia Manzan , Costa Júlia Gatti Ladeia , Pinheiro Breno Veloso , Vasconcelos-Santos Daniel Vitor , Ferreira Adriana Melo , Su Chunlei , Januário José Nélio , Vitor Ricardo Wagner Almeida 
Published: January 2013

ABSTRACT

Recent studies of
Toxoplasma gondii
isolates from animals in Brazil have revealed high genetic diversity. Many of these isolates are virulent to mice. It is speculated that these isolates may also be virulent to humans. However, there is very limited data regarding
T. gondii
strains from human infection. Therefore, it is not clear whether there is any association between parasite genotypes and disease phenotypes. In this study, a total of 27
T. gondii
strains were isolated from humans with congenital toxoplasmosis in Minas Gerais state, Brazil. The genetic variability was assessed by restricted fragment length polymorphism in 11 loci (
SAG1
, 5′ plus 3′
SAG2
, alternative [alt.]
SAG2
,
SAG3
,
BTUB
,
GRA6
,
c22-8
,
c29-2
,
L358
,
PK1
, and
Apico
). Genetic analysis of 24 strains revealed 14 different genotypes, including 7 previously identified from animals and 7 new types. The widespread genotype BrII accounted for 29% (7/24) of the isolates and was the dominant genotype involved in this study. This is the first report of genotyping of
T. gondii
isolates obtained from blood samples from newborns with congenital toxoplasmosis. Genotypic characterization of these isolates suggests high genetic diversity of
T. gondii
in this human population in Brazil. Future studies are needed to determine the source of contamination of this human population.
Yersinia enterocolitica in Diagnostic Fecal Samples from European Dogs and Cats: Identification by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Stamm Ivonne , Hailer Mandy , Depner Barbara , Kopp Peter A. , Rau Jörg 
Published: January 2013

ABSTRACTYersinia enterocoliticais the main cause of yersiniosis in Europe, one of the five main bacterial gastrointestinal diseases of humans. Beside pigs, companion animals, especially dogs and cats, were repeatedly discussed in the past as a possible source of pathogenicY. enterocolitica. To investigate the presence and types ofY. enterocoliticain companion animals, a total of 4,325 diagnostic fecal samples from dogs and 2,624 samples from cats were tested. The isolates obtained were differentiated by using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and Fourier transform infrared spectroscopy (FT-IR). IsolatedY. enterocoliticastrains were bioserotyped. The detection of theailgene by PCR and confirmation by FT-IR were used as a pathogenicity marker.Y. enterocoliticastrains were isolated from 198 (4.6%) of the dog and 8 (0.3%) of the cat fecal samples investigated. One hundred seventy-nine isolates from dogs were analyzed in detail. The virulence factor Ail was detected in 91.6% of isolates. Isolates of biotype 4 (54.7%) and, to a lesser extent, biotypes 2 (23.5%), 3 (11.2%), and 5 (2.2%) were detected. The remaining 8.4% of strains belonged to theail-negative biotype 1A. All 7 isolates from cats that were investigated in detail wereailpositive. These results indicate that companion animals could be a relevant reservoir for a broad range of presumptively human-pathogenicY. enterocoliticatypes. MALDI-TOF MS and FT-IR proved to be valuable methods for the rapid identification ofY. enterocolitica, especially in regard to the large number of samples that were investigated in a short time frame.
Evaluation of a Benchtop HIV Ultradeep Pyrosequencing Drug Resistance Assay in the Clinical Laboratory
Authors: Avidor Boaz , Girshengorn Shirley , Matus Natalia , Talio Hadass , Achsanov Svetlana , Zeldis Irene , Fratty Ilana S. , Katchman Eugene , Brosh-Nissimov Tal , Hassin David , Alon Danny , Bentwich Zvi , Yust Israel , Amit Sharon , Forer Relly , Vulih Shultsman Ina , Turner Dan 
Published: January 2013

ABSTRACT
Detection of low-abundance drug resistance mutations (DRMs) of HIV-1 is an evolving approach in clinical practice. Ultradeep pyrosequencing has shown to be effective in detecting such mutations. The lack of a standardized commercially based assay limits the wide use of this method in clinical settings. 454 Life Sciences (Roche) is developing an HIV ultradeep pyrosequencing assay for their benchtop sequencer. We assessed the prototype plate in the clinical laboratory. Plasma samples genotyped by the standardized TruGene kit were retrospectively tested by this assay. Drug-treated subjects failing therapy and drug-naive patients were included. DRM analysis was based on the International AIDS Society USA DRM list and the Stanford algorithm. The prototype assay detected all of the DRMs detected by TruGene and additional 50 low-abundance DRMs. Several patients had low-abundance D67N, K70R, and M184V reverse transcriptase inhibitor mutations that persisted long after discontinuation of the drug that elicited these mutations. Additional patient harbored low-abundance V32I major protease inhibitor mutation, which under darunavir selection evolved later to be detected by TruGene. Stanford analysis suggested that some of the low-abundance DRMs were likely to affect the resistance burden in these subjects. The prototype assay performs at least as well as TruGene and has the advantage of detecting low-abundance drug resistance mutations undetected by TruGene. Its ease of use and lab-scale platform will likely facilitate its use in the clinical laboratory. The extent to which the detection of low-abundance DRMs will affect patient management is still unknown, but it is hoped that use of such an assay in clinical practice will help resolve this important question.
Detection of the A2058G and A2059G 23S rRNA Gene Point Mutations Associated with Azithromycin Resistance in Treponema pallidum by Use of a TaqMan Real-Time Multiplex PCR Assay
Authors: Chen Cheng-Yen , Chi Kai-Hua , Pillay Allan , Nachamkin Eli , Su John R. , Ballard Ronald C. 
Published: January 2013

ABSTRACT

Macrolide treatment failure in syphilis patients is associated with a single point mutation (either A2058G or A2059G) in both copies of the 23S rRNA gene in
Treponema pallidum
strains. The conventional method for the detection of both point mutations uses nested PCR combined with restriction enzyme digestions, which is laborious and time-consuming. We initially developed a TaqMan-based real-time duplex PCR assay for detection of the A2058G mutation, and upon discovery of the A2059G mutation, we modified the assay into a triplex format to simultaneously detect both mutations. The point mutations detected by the real-time triplex PCR were confirmed by pyrosequencing. A total of 129 specimens PCR positive for
T. pallidum
that were obtained from an azithromycin resistance surveillance study conducted in the United States were analyzed. Sixty-six (51.2%) of the 129 samples with the A2058G mutation were identified by both real-time PCR assays. Of the remaining 63 samples that were identified as having a macrolide-susceptible genotype by the duplex PCR assay, 17 (27%) were found to contain the A2059G mutation by the triplex PCR. The proportions of macrolide-susceptible versus -resistant genotypes harboring either the A2058G or the A2059G mutation among the
T. pallidum
strains were 35.6, 51.2, and 13.2%, respectively. None of the
T. pallidum
strains examined had both point mutations. The TaqMan-based real-time triplex PCR assay offers an alternative to conventional nested PCR and restriction fragment length polymorphism analyses for the rapid detection of both point mutations associated with macrolide resistance in
T. pallidum
.
Evaluation of Brilliance MRSA 2 Agar for Detection of Methicillin-Resistant Staphylococcus aureus in Clinical Samples
Authors: Veenemans J. , Verhulst C. , Punselie R. , van Keulen P. H. J. , Kluytmans J. A. J. W. 
Published: January 2013

ABSTRACT

We compared 2 chromogenic media (Oxoid
Brilliance
MRSA 2 agar [Thermo Fisher Scientific] and MRSA-ID [bioMérieux]) for the detection of methicillin-resistant
Staphylococcus aureus
(MRSA) in 1,368 hospital samples. For both media, broth enrichment was essential to obtain satisfactory diagnostic performance. Although with direct cultures only, the diagnostic performance (particularly sensitivity) of
Brilliance
MRSA 2 agar appears better than that of MRSA-ID, no difference in sensitivity or specificity between the media was detected after inclusion of an enrichment step.
Most Influenza A Virions Fail To Express at Least One Essential Viral Protein
Authors: Brooke Christopher B. , Ince William L. , Wrammert Jens , Ahmed Rafi , Wilson Patrick C. , Bennink Jack R. , Yewdell Jonathan W. 
Published: January 2013

ABSTRACT
Segmentation of the influenza A virus (IAV) genome enables rapid gene reassortment at the cost of complicating the task of assembling the full viral genome. By simultaneously probing for the expression of multiple viral proteins in MDCK cells infected at a low multiplicity with IAV, we observe that the majority of infected cells lack detectable expression of one or more essential viral proteins. Consistent with this observation, up to 90% of IAV-infected cells fail to release infectious progeny, indicating that many IAV virions scored as noninfectious by traditional infectivity assays are capable of single-round infection. This fraction was not significantly affected by target or producer cell type but varied widely between different IAV strains. These data indicate that IAV exists primarily as a swarm of complementation-dependent semi-infectious virions, and thus traditional, propagation-dependent assays of infectivity may drastically misrepresent the true infectious potential of a virus population.
An Endothelial Cell-Specific Requirement for the
UL133-UL138
Locus of Human Cytomegalovirus for Efficient Virus Maturation
Authors: Bughio Farah , Elliott David A. , Goodrum Felicia 
Published: January 2013

ABSTRACT

Human cytomegalovirus (HCMV) infects a variety of cell types in humans, resulting in a varied pathogenesis in the immunocompromised host. Endothelial cells (ECs) are considered an important target of HCMV infection that may contribute to viral pathogenesis. Although the viral determinants important for entry into ECs are well defined, the molecular determinants regulating postentry tropism in ECs are not known. We previously identified the
UL133-UL138
locus encoded within the clinical strain-specific UL
b
′ region of the HCMV genome as important for the latent infection in CD34
+
hematopoietic progenitor cells (HPCs). Interestingly, this locus, while dispensable for replication in fibroblasts, was required for efficient replication in ECs infected with the TB40E or fusion-inducing factor X (FIX) HCMV strains. ECs infected with a virus lacking the entire locus (
UL133-UL138
NULL
virus) complete the immediate-early and early phases of infection but are defective for infectious progeny virus production. ECs infected with
UL133-UL138
NULL
virus exhibited striking differences in the organization of intracellular membranes and in the assembly of mature virions relative to ECs infected with wild-type (WT) virus. In
UL133-UL138
NULL
virus-infected ECs, Golgi stacks were disrupted, and the viral assembly compartment characteristic of HCMV infection failed to form. Further, progeny virions in
UL133-UL138
NULL
virus-infected ECs inefficiently acquired the virion tegument and secondary envelope. These defects were specific to infection in ECs and not observed in fibroblasts infected with
UL133-UL138
NULL
virus, suggesting an EC-specific requirement for the
UL133-UL138
locus for late stages of replication. To our knowledge, the
UL133-UL138
locus represents the first cell-type-dependent, postentry tropism determinant required for viral maturation.
Characterization of the Uukuniemi Virus Group (Phlebovirus: Bunyaviridae): Evidence for Seven Distinct Species
Authors: Palacios Gustavo , Savji Nazir , Travassos da Rosa Amelia , Guzman Hilda , Yu Xuejie , Desai Aaloki , Rosen Gail Emilia , Hutchison Stephen , Lipkin W. Ian , Tesh Robert 
Published: January 2013

ABSTRACT

Evolutionary insights into the phleboviruses are limited because of an imprecise classification scheme based on partial nucleotide sequences and scattered antigenic relationships. In this report, the serologic and phylogenetic relationships of the Uukuniemi group viruses and their relationships with other recently characterized tick-borne phleboviruses are described using full-length genome sequences. We propose that the viruses currently included in the
Uukuniemi virus
group be assigned to five different species as follows:
Uukuniemi virus
,
EgAn 1825-61 virus
,
Fin V707 virus
,
Chizé virus
, and
Zaliv Terpenia virus
would be classified into the
Uukuniemi
species;
Murre virus
,
RML-105-105355 virus
, and
Sunday Canyon virus
would be classified into a
Murre virus
species; and
Grand Arbaud virus
,
Precarious Point virus
, and
Manawa virus
would each be given individual species status. Although limited sequence similarity was detected between current members of the
Uukuniemi
group and
Severe fever with thrombocytopenia syndrome virus
(SFTSV) and
Heartland virus
, a clear serological reaction was observed between some of them, indicating that SFTSV and
Heartland virus
should be considered part of the
Uukuniemi virus
group. Moreover, based on the genomic diversity of the phleboviruses and given the low correlation observed between complement fixation titers and genetic distance, we propose a system for classification of the
Bunyaviridae
based on genetic as well as serological data. Finally, the recent descriptions of SFTSV and Heartland virus also indicate that the public health importance of the Uukuniemi group viruses must be reevaluated.
The Receptor-Binding Site of the Measles Virus Hemagglutinin Protein Itself Constitutes a Conserved Neutralizing Epitope
Authors: Tahara Maino , Ohno Shinji , Sakai Kouji , Ito Yuri , Fukuhara Hideo , Komase Katsuhiro , Brindley Melinda A. , Rota Paul A. , Plemper Richard K. , Maenaka Katsumi , Takeda Makoto 
Published: January 2013

ABSTRACT
Here, we provide direct evidence that the receptor-binding site of measles virus (MV) hemagglutinin protein itself forms an effective conserved neutralizing epitope (CNE). Several receptor-interacting residues constitute the CNE. Thus, viral escape from neutralization has to be associated with loss of receptor-binding activity. Since interactions with both the signaling lymphocyte activation molecule (SLAM) and nectin4 are critical for MV pathogenesis, its escape, which results from loss of receptor-binding activity, should not occur in nature.
Individual N-Glycans Added at Intervals along the Stalk of the Nipah Virus G Protein Prevent Fusion but Do Not Block the Interaction with the Homologous F Protein
Authors: Zhu Qiyun , Biering Scott B. , Mirza Anne M. , Grasseschi Brittany A. , Mahon Paul J. , Lee Benhur , Aguilar Hector C. , Iorio Ronald M. 
Published: January 2013

ABSTRACT
The promotion of membrane fusion by most paramyxoviruses requires an interaction between the viral attachment and fusion (F) proteins to enable receptor binding by the former to trigger the activation of the latter for fusion. Numerous studies demonstrate that the F-interactive sites on the Newcastle disease virus (NDV) hemagglutinin-neuraminidase (HN) and measles virus (MV) hemagglutinin (H) proteins reside entirely within the stalk regions of those proteins. Indeed, stalk residues of NDV HN and MV H that likely mediate the F interaction have been identified. However, despite extensive efforts, the F-interactive site(s) on the Nipah virus (NiV) G attachment glycoprotein has not been identified. In this study, we have introduced individual N-linked glycosylation sites at several positions spaced at intervals along the stalk of the NiV G protein. Five of the seven introduced sites are utilized as established by a retardation of electrophoretic mobility. Despite surface expression, ephrinB2 binding, and oligomerization comparable to those of the wild-type protein, four of the five added N-glycans completely eliminate the ability of the G protein to complement the homologous F protein in the promotion of fusion. The most membrane-proximal added N-glycan reduces fusion by 80%. However, unlike similar NDV HN and MV H mutants, the NiV G glycosylation stalk mutants retain the ability to bind F, indicating that the fusion deficiency of these mutants is not due to prevention of the G-F interaction. These findings suggest that the G-F interaction is not mediated entirely by the stalk domain of G and may be more complex than that of HN/H-F.
Social responsibility in the information society
Authors: Taylor Richard 
Published: January 2013

The technical advances that have enabled the development of "the cloud" have resulted in an exponential increase in the speed of information dissemination. Policy makers, sponsors of IT infrastructure and users of information and communication technologies, while being aware of the benefits of "the Cloud" as a mechanism to facilitate more efficient access to information, do not always appreciate that these developments may not always have the positive outcomes intended.
University courses such as those in Social Informatics have managed to keep pace with this rapid evolution of information and communication technologies and their societal impacts, but within the secondary education sector this has not always been possible, potentially creating a knowledge gap for tomorrow's policy makers.
Chloroquine in Cancer Therapy: A Double-Edged Sword of Autophagy
Authors: Kimura Tomonori , Takabatake Yoshitsugu , Takahashi Atsushi , Isaka Yoshitaka 
Published: January 2013

Abstract
Autophagy is a homeostatic cellular recycling system that is responsible for degrading damaged or unnecessary cellular organelles and proteins. Cancer cells are thought to use autophagy as a source of energy in the unfavorable metastatic environment, and a number of clinical trials are now revealing the promising role of chloroquine, an autophagy inhibitor, as a novel antitumor drug. On the other hand, however, the kidneys are highly vulnerable to chemotherapeutic agents. Recent studies have shown that autophagy plays a protective role against acute kidney injury, including cisplatin-induced kidney injury, and thus, we suspect that the use of chloroquine in combination with anticancer drugs may exacerbate kidney damage. Moreover, organs in which autophagy also plays a homeostatic role, such as the neurons, liver, hematopoietic stem cells, and heart, may be sensitive to the combined use of chloroquine and anticancer drugs. Here, we summarize the functions of autophagy in cancer and kidney injury, especially focusing on the use of chloroquine to treat cancer, and address the possible side effects in the combined use of chloroquine and anticancer drugs. Cancer Res; 73(1); 3–7. ©2012 AACR.