bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Price Theory of Vertical and Lateral Integration*
Authors: Legros Patrick , Newman Andrew F. 
Published: December 2012

Abstract
This article presents a perfectly competitive model of firm boundary decisions and study their interplay with product demand, technology, and welfare. Integration is privately costly but is effective at coordinating production decisions; nonintegration is less costly but coordinates relatively poorly. Output price influences the choice of ownership structure: integration increases with the price level. At the same time, ownership affects output, because integration is more productive than nonintegration. For a generic set of demand functions, equilibrium delivers heterogeneity of ownership and performance among ex ante identical enterprises. The price mechanism transmutes demand shifts into industry-wide reorganizations and generates external effects from technological shocks: productivity changes in some firms may induce ownership changes in others. If the enterprise managers have full title to its revenues, market equilibrium ownership structures are second-best efficient. When managers have less than full revenue claims, equilibrium can be inefficient, with too little integration.
Dynamic Behavior of a Large Ring of Coupled Self-Excited Oscillators
Authors: Barron Miguel A. , Sen Mihir 
Published: December 2012

Abstract
Interconnected, self-excited oscillators are often found in nature and in engineered devices. In this work, a ring of van der Pol oscillators, each of which is connected to its immediate neighbors, is considered. The focus is on the emergent behavior of a large number of oscillators. Conditions are determined under which time-independent solutions are obtained, and the linear stability of these solutions is investigated. The effect of the singularity of the coupling matrix on the ring dynamics is explored. When this becomes singular, an infinite number of steady states is present, and the phenomenon of oscillation death arises. It is also possible to have, depending on initial conditions, all oscillators with in-phase synchrony, metachronal traveling waves with different wavelengths going around the ring, or standing waves. Interconnected oscillators can propagate information at a group velocity, and the information signal is present as an amplitude modulation.
Normal and shear strain imaging using 2D deformation tracking on beam steered linear array datasets
Authors: Xu Haiyan , Varghese Tomy 
Published: December 2012

Purpose:Previous publications have reported on the use of one‐dimensional cross‐correlation analysis with beam‐steered echo signals. However, this approach fails to accurately track displacements at larger depths (>4.5 cm) due to lower signal‐to‐noise. In this paper, the authors present the use of adaptive parallelogram shaped two‐dimensional processing blocks for deformation tracking.Methods:Beam‐steered datasets were acquired using a VFX 9L4 linear array transducer operated at a 6 MHz center frequency for steered angles from −15 to 15° in increments of 1°, on both uniformly elastic and single‐inclusion tissue‐mimicking phantoms. Echo signals were acquired to a depth of 65 mm with the focus set at 40 mm corresponding to the center of phantom. Estimated angular displacements along and perpendicular to the beam direction are used to compute axial and lateral displacement vectors using a least‐squares approach. Normal and shear strain tensor component are then estimated based on these displacement vectors.Results:Their results demonstrate that parallelogram shaped two‐dimensional deformation tracking significantly improves spatial resolution (factor of 7.79 along the beam direction), signal‐to‐noise (5 dB improvement), and contrast‐to‐noise (8–14 dB improvement) associated with strain imaging using beam steering on linear array transducers.Conclusions:Parallelogram shaped two‐dimensional deformation tracking is demonstrated in beam‐steered radiofrequency data, enabling its use in the estimation of normal and shear strain components.
Real‐time automatic fiducial marker tracking in low contrast cine‐MV images
Authors: Lin Wei‐Yang , Lin Shu‐Fang , Yang Sheng‐Chang , Liou Shu‐Cheng , Nath Ravinder , Liu Wu 
Published: December 2012

Purpose:To develop a real‐time automatic method for tracking implanted radiographic markers in low‐contrast cine‐MV patient images used in image‐guided radiation therapy (IGRT).Methods:Intrafraction motion tracking using radiotherapy beam‐line MV images have gained some attention recently in IGRT because no additional imaging dose is introduced. However, MV images have much lower contrast than kV images, therefore a robust and automatic algorithm for marker detection in MV images is a prerequisite. Previous marker detection methods are all based on template matching or its derivatives. Template matching needs to match object shape that changes significantly for different implantation and projection angle. While these methods require a large number of templates to cover various situations, they are often forced to use a smaller number of templates to reduce the computation load because their methods all require exhaustive search in the region of interest. The authors solve this problem by synergetic use of modern but well‐tested computer vision and artificial intelligence techniques; specifically the authors detect implanted markers utilizing discriminant analysis for initialization and use mean‐shift feature space analysis for sequential tracking. This novel approach avoids exhaustive search by exploiting the temporal correlation between consecutive frames and makes it possible to perform more sophisticated detection at the beginning to improve the accuracy, followed by ultrafast sequential tracking after the initialization. The method was evaluated and validated using 1149 cine‐MV images from two prostate IGRT patients and compared with manual marker detection results from six researchers. The average of the manual detection results is considered as the ground truth for comparisons.Results:The average root‐mean‐square errors of our real‐time automatic tracking method from the ground truth are 1.9 and 2.1 pixels for the two patients (0.26 mm/pixel). The standard deviations of the results from the 6 researchers are 2.3 and 2.6 pixels. The proposed framework takes about 128 ms to detect four markers in the first MV images and about 23 ms to track these markers in each of the subsequent images.Conclusions:The unified framework for tracking of multiple markers presented here can achieve marker detection accuracy similar to manual detection even in low‐contrast cine‐MV images. It can cope with shape deformations of fiducial markers at different gantry angles. The fast processing speed reduces the image processing portion of the system latency, therefore can improve the performance of real‐time motion compensation.
Characterization of Recombinant Per a 10 from Periplaneta americana
Authors: Govindaraj Dhanapal , Gaur Shailendra Nath , Arora Naveen 
Published: December 2012

ABSTRACT

Cockroach allergen is a major risk factor for IgE-mediated allergic response and asthma in sensitized individuals. Serine proteases have been identified from various sources and characterized as major allergens. The present study was aimed to express and characterize recombinant allergen Per a 10 (rPer a 10) from
Periplaneta americana.
rPer a 10 was expressed in
Escherichia coli
and purified in soluble form, yielding 0.75 mg/liter of culture. Homology of the Per a 10 protein sequence exhibited 27 to 38% similarity to the mite serine protease and 41 to 52% similarity to other insect trypsins. The purified rPer a 10 protein resolved at 28 kDa on SDS-PAGE and was recognized by cockroach-hypersensitive patients' sera by immunoblotting and enzyme-linked immunosorbent assay (ELISA). In competitive ELISA, rPer a 10 required 96 ng of purified protein for 50% inhibition of IgE binding, whereas 34 ng of native protein (nPer a 10) was required for the same inhibition. rPer a 10 and nPer a 10 induced basophil histamine release in the range of 47 to 64% and 60 to 85%, respectively, when sensitized with cockroach-hypersensitive patients' sera. In conclusion, Per a 10 was subcloned, and the protein was purified to homogeneity. rPer a 10 showed reduced IgE binding and histamine release and showed no proteolytic activity. These data suggest that rPer a 10 has potential for immunotherapy.
Single Real-Time Reverse Transcription-PCR Assay for Detection and Quantification of Genetically Diverse HIV-1, SIVcpz, and SIVgor Strains
Authors: Etienne Lucie , Eymard-Duvernay Sabrina , Aghokeng Avelin , Butel Christelle , Monleau Marjorie , Peeters Martine 
Published: December 2012

ABSTRACT

Although antiretroviral treatment availability has improved, the virological monitoring of patients remains largely uneven across regions. In addition, viral quantification tests are suffering from human immunodeficiency virus type 1 (HIV-1) genetic diversity, fueled by the emergence of new recombinants and of lentiviruses from nonhuman primates. We developed a real-time reverse transcription-PCR (RT-PCR) assay that is relatively inexpensive and able to detect and quantify all circulating forms of HIV-1 and its simian immunodeficiency virus (SIV) precursors, SIVcpz and SIVgor. Primers and a probe were designed to detect all variants of the HIV-1/SIVcpz/SIVgor lineage. HIV-1 M plasma (
n
= 190; 1.68 to 7.78 log
10
copies/ml) representing eight subtypes, nine circulating recombinant forms, and 21 unique recombinant forms were tested. The mean PCR efficiency was 99%, with low coefficients of intra- and interassay variation (<5%) and a limit of quantification of <2.50 log
10
copies/ml, with a 200-μl plasma volume. On the studied range, the specificity and the analytical sensitivity were 100 and 97.4%, respectively. The viral loads were highly correlated (
r
= 0.95,
P
< 0.0001) with the reference method (generic HIV assay; Biocentric) and had no systematic difference, irrespective of genotype. Furthermore, 22 HIV-1 O plasmas were screened and were better quantified compared to the gold-standard RealTime HIV-1 assay (Abbott), including four samples that were only quantified by our assay. Finally, we could quantify SIVcpzPtt and SIVcpzPts from chimpanzee plasma (
n
= 5) and amplify SIVcpz and SIVgor from feces. Thus, the newly developed real-time RT-PCR assay detects and quantifies strains from the HIV-1/SIVcpz/SIVgor lineage, including a wide diversity of group M strains and HIV-1 O. It can therefore be useful in geographical areas of high HIV diversity and at risk for the emergence of new HIV variants.
An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of
vif
mRNA
Authors: Widera Marek , Erkelenz Steffen , Hillebrand Frank , Krikoni Aikaterini , Widera Darius , Kaisers Wolfgang , Deenen René , Gombert Michael , Dellen Rafael , Pfeiffer Tanya , Kaltschmidt Barbara , Münk Carsten , Bosch Valerie , Köhrer Karl , Schaal Heiner 
Published: December 2012

ABSTRACT

Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3′ splice site (3′ss) A1 but lack splicing at 5′ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3′ss A1 and repression of D2, respectively, determine the levels of
vif
mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3′ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5′ss D2. Here we show that an intronic G run (G
I2
-1) represses the use of a second 5′ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G
I2
-1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of
vif
mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vif-to-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here.
Effects of an Early Conformational Switch Defect during ϕX174 Morphogenesis Are Belatedly Manifested Late in the Assembly Pathway
Authors: Gordon Emile B. , Fane Bentley A. 
Published: December 2012

ABSTRACT

C-terminal, aromatic amino acids in the ϕX174 internal scaffolding protein B mediate conformational switches in the viral coat protein. These switches direct the coat protein through early assembly. In addition to the aromatic amino acids, two acidic residues, D111 and E113, form salt bridges with basic, coat protein side chains. Although salt bridge formation did not appear to be critical for assembly, the substitution of an aromatic amino acid for D111 produced a lethal phenotype. This side chain is uniquely oriented toward the center of the coat-scaffolding binding pocket, which is heavily dominated by aromatic ring-ring interactions. Thus, the D111Y substitution may restructure pocket contacts. Previously characterized
B
−
mutants blocked assembly before procapsid formation. However, the D111Y mutant produced an assembled particle, which contained the structural and external scaffolding proteins but lacked protein B and DNA. A suppressor within the external scaffolding protein, which mediates the later stages of particle morphogenesis, restored viability. The unique formation of a postprocapsid particle and the novel suppressor may be indicative of a novel B protein function. However, genetic data suggest that the particle represents the delayed manifestation of an early assembly error. This seemingly late-acting defect was rescued by previously characterized suppressors of early, preprocapsid,
B
−
assembly mutations, which act on the level of coat protein flexibility. Likewise, the newly isolated suppressor in the external scaffolding protein also exhibited a global suppressing phenotype. Thus, the off-pathway product isolated from infected cells may not accurately reflect the temporal nature of the initial defect.
Tropism and Infectivity of Influenza Virus, Including Highly Pathogenic Avian H5N1 Virus, in Ferret Tracheal Differentiated Primary Epithelial Cell Cultures
Authors: Zeng Hui , Goldsmith Cynthia S. , Maines Taronna R. , Belser Jessica A. , Gustin Kortney M. , Pekosz Andrew , Zaki Sherif R. , Katz Jacqueline M. , Tumpey Terrence M. 
Published: December 2012

ABSTRACT

Tropism and adaptation of influenza viruses to new hosts is partly dependent on the distribution of the sialic acid (SA) receptors to which the viral hemagglutinin (HA) binds. Ferrets have been established as a valuable
in vivo
model of influenza virus pathogenesis and transmission because of similarities to humans in the distribution of HA receptors and in clinical signs of infection. In this study, we developed a ferret tracheal differentiated primary epithelial cell culture model that consisted of a layered epithelium structure with ciliated and nonciliated cells on its apical surface. We found that human-like (α2,6-linked) receptors predominated on ciliated cells, whereas avian-like (α2,3-linked) receptors, which were less abundant, were presented on nonciliated cells. When we compared the tropism and infectivity of three human (H1 and H3) and two avian (H1 and H5) influenza viruses, we observed that the human influenza viruses primarily infected ciliated cells and replicated efficiently, whereas a highly pathogenic avian H5N1 virus (A/Vietnam/1203/2004) replicated efficiently within nonciliated cells despite a low initial infection rate. Furthermore, compared to other influenza viruses tested, VN/1203 virus replicated more efficiently in cells isolated from the lower trachea and at a higher temperature (37°C) compared to a lower temperature (33°C). VN/1203 virus infection also induced higher levels of immune mediator genes and cell death, and virus was recovered from the basolateral side of the cell monolayer. This ferret tracheal differentiated primary epithelial cell culture system provides a valuable
in vitro
model for studying cellular tropism, infectivity, and the pathogenesis of influenza viruses.
CD4 T-Cell Memory Responses to Viral Infections of Humans Show Pronounced Immunodominance Independent of Duration or Viral Persistence
Authors: Jing Lichen , Schiffer Joshua T. , Chong Tiana M. , Bruckner Joseph J. , Davies D. Huw , Felgner Phillip L. , Haas Juergen , Wald Anna , Verjans G. M. G. M. , Koelle David M. 
Published: December 2012

ABSTRACTLittle is known concerning immunodominance within the CD4 T-cell response to viral infections and its persistence into long-term memory. We tested CD4 T-cell reactivity against each viral protein in persons immunized with vaccinia virus (VV), either recently or more than 40 years ago, as a model self-limited viral infection. Similar tests were done with persons with herpes simplex virus 1 (HSV-1) infection as a model chronic infection. We used an indirect method capable of counting the CD4 T cells in blood reactive with each individual viral protein. Each person had a clear CD4 T-cell dominance hierarchy. The top four open reading frames accounted for about 40% of CD4 virus-specific T cells. Early and long-term memory CD4 T-cell responses to vaccinia virus were mathematically indistinguishable for antigen breadth and immunodominance. Despite the chronic intermittent presence of HSV-1 antigen, the CD4 T-cell dominance and diversity patterns for HSV-1 were identical to those observed for vaccinia virus. The immunodominant CD4 T-cell antigens included both long proteins abundantly present in virions and shorter, nonstructural proteins. Limited epitope level and directex vivodata were also consistent with pronounced CD4 T-cell immunodominance. We conclude that human memory CD4 T-cell responses show a pattern of pronounced immunodominance for both chronic and self-limited viral infections and that this pattern can persist over several decades in the absence of antigen.
A Short
cis
-Acting Motif in the M112-113 Promoter Region Is Essential for IE3 To Activate M112-113 Gene Expression and Is Important for Murine Cytomegalovirus Replication
Authors: Perez Kareni J. , Martínez Francisco Puerta , Cosme-Cruz Ruth , Perez-Crespo Neysa M. , Tang Qiyi 
Published: December 2012

ABSTRACT

Immediate-early 3 (IE3) gene products are required to activate early (E)-stage gene expression of murine cytomegaloviruses (MCMV). The first early gene activated by IE3 is the M112-113 gene (also called E1), although a complete understanding of the activation mechanism is still lacking. In this paper, we identify a 10-bp
cis
-regulating motif upstream of the M112-113 TATA box as important for IE3 activation of M112-113 expression. Results from DNA affinity assays and chromatin immunoprecipitation assays show that the association of IE3 with the M112-113 gene promoter was eliminated by deletion of the 10-bp DNA sequence, now named IE3AM (for IE3
a
ctivating
m
otif). In addition, IE3 interacts with TATA box binding protein (TBP), a core protein of TFIID (transcription initiation) complexes. Finally, we created an IE3AM-deleted MCMV (MCMVdIE3AM) using a bacterial artificial chromosome system. The mutant virus can still replicate in NIH 3T3 cells but at a significantly lower level. The defectiveness of the MCMVdIE3AM infection can be rescued in an M112-113-complemented cell line. Our results suggest that the interactions of IE3 with IE3AM and with TBP stabilize the TFIID complex at the M112-113 promoter such that M112-113 gene expression can be activated and/or enhanced.
Initial experience of a novel sheath guide for transbrachial carotid artery stenting: technical note
Authors: Iwata Tomonori , Mori Takahisa , Miyazaki Yuichi , Nakazaki Masahito , Takahashi Yoichiro , Mizokami Koji 
Published: December 2012

BackgroundThe transfemoral approach has been a common technique for carotid artery stenting (CAS). When aortic or peripheral arterial conditions limit the transfemoral approach, the transbrachial approach may be used as an alternative. The purpose of our study was to report initial experiences of CAS with a novel sheath guide specifically designed for transbrachial carotid cannulation.MethodsPatients who underwent transbrachial CAS with a novel sheath guide between May 2011 and July 2012 were analyzed. The sheath guide has an internal diameter of 6 Fr (2.24 mm, 0.088 inch) and is 90 cm long with a soft distal part and a particular distal shape like a modified Simmons catheter.ResultsSixty-two patients underwent transbrachial CAS with the sheath guide. Transbrachial carotid cannulation was easy and successful and CAS procedures were performed easily through the sheath guide in every case. No sheath-related periprocedural complications occurred.ConclusionsThe sheath guide specifically designed for transbrachial carotid cannulation is useful for transbrachial CAS.
Re-production at Stake: Experiences of Family Planning and Fertility among Amdo Tibetan Women
Authors: Schrempf Mona 
Published: December 2012

Abstract
Biographical interviews with Tibetan women in rural Amdo (Qinghai Province,
China) indicate that many women above 40 years of age experienced family
planning as a threat to their reproductive health, social status and economic
production. Even though family planning, implemented since 1980, was experienced
differently among the targeted women, they nevertheless addressed the same
social pressure of having to reconcile normative birth control administered by
the Chinese state with Tibetan socio-cultural norms and values of fertility
focused upon preferences for sons. Renowned female Tibetan doctors in private
and public clinics and hospitals were Tibetan women’s preferred and
trusted addressees for voluntary birth control and reproductive health. I argue
therefore, that in order to understand the effects of family planning on
targeted Tibetan women, socio-cultural values of fertility need to be taken into
account as they are expressed in women’s narratives of their
bio-psycho-social, gendered and ethnic selves.
‘Female Nectar’: A Study of Hybridity and Gender in Contemporary Tibetan Medical Literature on Menstruation
Authors: Bright Jenny 
Published: December 2012

Abstract
This essay examines contemporary Tibetan medical literature that deals with
menstruation, focusing on the relations among medical, religious and cultural
perceptions of women and gender. Present-day medical writers present a hybrid
account of menstruation, incorporating key aspects of Tibetan medicine, such as
the refining processes of digestion and the red element, with biomedical
knowledge, notably the role of hormones. The integration of biomedical thought
by Tibetan writers works to substantiate and bolster the validity of Tibetan
medical claims, rather than discredit them. Consequently, contemporary writers
are able to articulate medical knowledge about women that is as much about
Tibetan religious and cultural perceptions of gender and sexed-bodies, as it is
‘scientific’.
Impact of oxygen concentration on growth of mesenchymal stromal cells from the marrow of patients with chronic lymphocytic leukemia
Authors: Fecteau Jessie-F. , Messmer Davorka , Zhang Suping , Cui Bing , Chen Liguang , Kipps Thomas J. 
Published: December 2012

Key Points
Physiologic O2 levels in vitro enhance the propagation and function of mesenchymal stromal cells from chronic lymphocytic leukemia patients.