bluuebunny/crossref_metadata_2025 huggingface dataset:
Transient Solutions to Groundwater Mounding in Bounded and Unbounded Aquifers
Authors: Korkmaz Serdar
Published: September 2012

In this study, the well‐known Hantush solution procedure for groundwater mounding under infinitely long infiltration strips is extended to finite and semi‐infinite aquifer cases. Initially, the solution for infinite aquifers is presented and compared to those available in literature and to the numerical results of MODFLOW. For the finite aquifer case, the method of images, which is commonly used in well hydraulics, is used to be able to represent the constant‐head boundaries at both sides. It is shown that a finite number of images is enough to obtain the results and sustain the steady state. The effect of parameters on the growth of the mound and on the time required to reach the steady state is investigated. The semi‐infinite aquifer case is emphasized because the growth of the mound is not symmetric. As the constant‐head boundary limits the growth, the unbounded side grows continuously. For this reason, the groundwater divide shifts toward the unbounded side. An iterative solution procedure is proposed. To perform the necessary computations a code was written in Visual Basic of which the algorithm is presented. The proposed methodology has a wide range of applicability and this is demonstrated using two practical examples. The first one is mounding under a stormwater dispersion trench in an infinite aquifer and the other is infiltration from a flood control channel into a semi‐infinite aquifer. Results fit very well with those of MODFLOW.
DEALERS, THIEVES, AND THE COMMON DETERMINANTS OF DRUG AND NONDRUG ILLEGAL EARNINGS*
Authors: THOMPSON MELISSA , UGGEN CHRISTOPHER
Published: September 2012

Drug crime often is viewed as distinctive from other types of crime, meriting greater or lesser punishment. In view of this special status, this article asks whether and how illegal earnings attainment differs between drug sales and other forms of economic crime. We estimate monthly illegal earnings with fixed‐effects models, based on data from the National Supported Work Demonstration Project and the National Longitudinal Survey of Youth. Although drug sales clearly differ from other types of income‐generating crime, we find few differences in their determinants. For example, the use of cocaine or heroin increases illegal earnings from both drug and nondrug crimes, indicating some degree of fungibility in the sources of illegal income. More generally, the same set of factors—particularly legal and illegal opportunities and embeddedness in criminal and conventional networks—predicts both drug earnings and nondrug illegal earnings.
NEIGHBORHOOD HOUSING INVESTMENTS AND VIOLENT CRIME IN SEATTLE, 1981–2007*
Authors: VÉLEZ MARÍA B. , LYONS CHRISTOPHER J. , BOURSAW BLAKE
Published: September 2012

Despite significant advances in the study of neighborhoods and crime, criminologists have paid surprisingly less attention to the extralocal forces that shape violence. To address this issue, we draw on an emerging body of work that stresses the role of home mortgage lending—a resource secured via interaction with external actors—in reducing neighborhood violence and extend it by addressing concerns that the lending–violence relationship is spurious and confounded by simultaneity. We explore the longitudinal relationship between residential mortgage lending and violence in Seattle with a pooled time series of 118 census tracts over 27 years, and we instrument our endogenous predictors (home mortgage lending and violent crime) with changes in their levels from prior periods. Employing Arellano–Bond difference models, we assess both the effect of mortgage lending on violent crime as well as the effect of violent crime levels on mortgage activity. We find that infusions of home mortgage lending yield reductions in subsequent violent crime; yet the impact of violent crime on subsequent lending is not significant. Results underscore the importance of incorporating external forces such as home mortgage lending into explanations of neighborhood violence.
ADOLESCENT VIOLENT VICTIMIZATION AND PRECOCIOUS UNION FORMATION*
Authors: KUHL DANIELLE C. , WARNER DAVID F. , WILCZAK ANDREW
Published: September 2012

This article bridges scholarship in criminology and family sociology by extending arguments about “precocious exits” from adolescence to consider early union formation as a salient outcome of violent victimization for youths. Research indicates that early union formation is associated with several negative outcomes; yet the absence of attention to union formation as a consequence of violent victimization is noteworthy. We address this gap by drawing on life course theory and data from the National Longitudinal Study of Adolescent Health (Add Health) to examine the effect of violent victimization (“street” violence) on the timing of first coresidential union formation—differentiating between marriage and cohabitation—in young adulthood. Estimates from Cox proportional hazard models show that adolescent victims of street violence experience higher rates of first union formation, especially marriage, early in the transition to adulthood; however, this effect declines with age, as such unions become more normative. Importantly, the effect of violent victimization on first union timing is robust to controls for nonviolent delinquency, substance abuse, and violent perpetration. We conclude by discussing directions for future research on the association between violent victimization and coresidential unions with an eye toward the implications of such early union formation for desistance.
Aurora Kinase B Is a Potential Therapeutic Target in Pediatric Diffuse Intrinsic Pontine Glioma
Authors: Buczkowicz Pawel , Zarghooni Maryam , Bartels Ute , Morrison Andrew , Misuraca Katherine L. , Chan Tiffany , Bouffet Eric , Huang Annie , Becher Oren , Hawkins Cynthia
Published: September 2012

Pediatric high‐grade astrocytomas (HGAs) account for 15–20% of all pediatric central nervous system tumors. These neoplasms predominantly involve the supratentorial hemispheres or the pons—diffuse intrinsic pontine gliomas (DIPG). Assumptions that pediatric HGAs are biologically similar to adult HGAs have recently been challenged, and the development of effective therapeutic modalities for DIPG and supratentorial HGA hinges on a better understanding of their biological properties. Here, 20 pediatric HGAs (9 DIPGs and 11 supratentorial HGAs) were subject to gene expression profiling following approval by the research ethics board at our institution. Many of these tumors showed expression signatures composed of genes that promote G1/S and G2/M cell cycle progression. In particular, Aurora kinase B (AURKB) was consistently and highly overexpressed in 6/9 DIPGs and 8/11 HGAs. Array data were validated using quantitative real‐time PCR and immunohistochemistry, as well as cross‐validation of our data set with previously published series. Inhibition of Aurora B activity in DIPG and in pediatric HGA cell lines resulted in growth arrest accompanied by morphological changes, cell cycle aberrations, nuclear fractionation and polyploidy as well as a reduction in colony formation. Our data highlight Aurora B as a potential therapeutic target in DIPG.
Identification of Ros Produced by Photodynamic Activity of Chlorophyll/Cyclodextrin Inclusion Complexes
Authors: Cellamare Barbara M. , Fini Paola , Agostiano Angela , Sortino Salvatore , Cosma Pinalysa
Published: September 2012

Photodynamic therapy (PDT) is a way of treating malignant tumors and hyperproliferative diseases. It is based on the use of photosensitizer, herein the chlorophyll a (chl a), and a light of an appropriate wavelength. The interaction of the photosensitizer (PS) with the light produces reactive oxygen species (ROS), powerful oxidizing agents, which cause critical damage to the tissue. To solubilize chl a in aqueous solution and to obtain it as monomer, we have used cyclodextrins, carriers which are able to interact with the pigment and form the inclusion complex. The aim of this study is to examine which types of ROS are formed by Chl a/cyclodextrin complexes in phosphate buffered solution and cell culture medium, using specific molecules, called primary acceptors, which react selectively with the reactive species. In fact the changes of the absorption and the emission spectra of these molecules after the illumination of the PS provide information on the specific ROS formation. The 1O2 formation has been tested using chemical methods based on the use of Uric Acid (UA), 9,10‐diphenilanthracene (DPA) and Singlet oxygen sensor green (SOSG) and by direct detection of Singlet Oxygen (1O2) luminescence decay at 1270 nm. Moreover, 2,7‐dichlorofluorescin and ferricytochrome c (Cyt Fe3+) have been used to detect the formation of hydrogen peroxide and superoxide radical anion, which reduces Fe3+ of the ferricytochrome to Fe2+, respectively.
Family structure, socioeconomic position and utilization of oral health services among Nigerian senior secondary school pupils
Authors: Ola Dennis , Gambôa Ana B. O. , Folayan Morenike O. , Marcenes Wagner
Published: September 2012

Objective: To test the relationship between socioeconomic position (SEP), family composition, number of siblings, and birth position in the family, and the utilization of oral health services by senior secondary school pupils in Ile‐Ife, Nigeria.

Methods: A cross‐sectional study design included senior secondary school pupils in the Central Local Government Area of Ile‐Ife during 2007/2008. Sample size calculation was performed and 1,200 pupils were invited to participate. A multistage, stratified sampling technique was used. Data collection included a self‐administered questionnaire. Data were analyzed using logistic regression.

Results: The response rate was 76 percent (n = 1043). The mean age was 15.8 (standard deviation = 1.9) and 49 percent were males. Only 22.5 percent of pupils had ever visited a dentist in their lives. Results from multivariate analyses showed that pupils attending free schools, those paying 1 to 10,000 naira (equivalent to US$ 63.31) and 10,000 to 19,000 naira (equivalent to US$ 120.29) were respectively 1.93, 1.87, and 2.74 times less likely to have attended a dentist in the past than pupils in more expensive schools. Pupils living with single mothers or without a parent were unlikely to have visited the dentist. Number of siblings and birth position in the family were not associated with utilization of oral health services.

Conclusions: Adolescents from families with a low SEP growing up without their parents may need extra incentives to visit dentist.
Proportion and extent of manifestation of molar‐incisor‐hypomineralizations according to different phenotypes
Authors: Kühnisch Jan , Heitmüller Daniela , Thiering Elisabeth , Brockow Inken , Hoffmann Ute , Neumann Claudia , Heinrich‐Weltzien Roswitha , Bauer Carl Peter , von Berg Andrea , Koletzko Sybille , Garcia‐Godoy Franklin , Hickel Reinhard , Heinrich Joachim
Published: September 2012

Objective: This epidemiological study aimed to assess the proportion and extent of manifestation of enamel hypomineralization, including molar‐incisor‐hypomineralization (MIH), in the permanent and primary dentition.

Methods: A total of 693 children enrolled in an ongoing birth cohort study (GINIplus‐10) were examined at their 10‐year follow‐up. Enamel hypomineralization was scored in the primary and permanent dentition on a tooth‐ and surface‐related level based on the criteria of the European Academy of Paediatric Dentistry (EAPD). Children were grouped according to their distribution pattern of enamel hypomineralization: children with a minimum of one hypomineralized tooth in the primary dentition (ht ≥ 1) and permanent dentition (HT ≥ 1); with a minimum of one hypomineralization on at least one first permanent molar (MIH); and with hypomineralization on at least one first permanent molar and permanent incisor (M + IH). For each group, the mean values of hypomineralized primary teeth (ht), permanent teeth (HT), and permanent surfaces (HS) were calculated.

Results: The proportion of affected children was 36.5 percent (HT ≥ 1), 14.7 percent (MIH), and 9.4 percent (M + IH); 6.9 percent of the subjects had a minimum of one affected primary tooth (ht ≥ 1). The mean number of hypomineralized permanent teeth and surfaces were 2.3HT/2.9HS (HT ≥ 1), 3.4HT/4.8HS (MIH), and 4.2HT/5.9HS (M + IH). The mean number of hypomineralized primary teeth amounted to 0.1ht in the entire study population.

Conclusions: Enamel hypomineralization can be detected frequently in this study sample. Children with M + IH showed the highest number of affected teeth and surfaces followed by those with MIH.
Measurement of choroidal perfusion and thickness following systemic sildenafil (Viagra®)
Authors: Kim David Y. , Silverman Ronald H. , Chan Robison Vernon Paul , Khanifar Aziz A. , Rondeau Mark , Lloyd Harriet , Schlegel Peter , Coleman Donald Jackson
Published: September 2012

Purpose:  To demonstrate anatomic and physiologic changes in the human choroid following systemic sildenafil citrate (Viagra®) using enhanced depth imaging spectral domain–optical coherence tomography (EDI‐OCT) and swept‐scan high‐frequency digital ultrasound.

Methods:  Seven healthy male subjects (mean age 32.7 years) were evaluated at baseline and 2 hr after ingesting 50 mg of sildenafil. Swept‐scan high‐frequency digital ultrasound and EDI‐OCT were utilized to measure choroidal perfusion and thickness, respectively. Results were read by masked observers. The Wilcoxon signed‐rank test and t‐test were used to analyse differences in choroidal flow and thickness at baseline and 2 hr after ingestion of sildenafil.

Results:  Two hours following sildenafil, increased choroidal perfusion was observed in 11 of 12 eyes measured by swept‐scan high‐frequency digital ultrasound. The mean increase was 3.46 (±2.00) times baseline with a range of 0.47–7.80 times baseline (p = 0.004). Increased choroidal thickness was observed in 12 of 12 eyes measured with EDI‐OCT. The average choroidal thickness increased by 11.6% temporal to the fovea, 9.3% nasal to the fovea and 10.7% underneath the fovea (p < 0.001 for all values).

Conclusions:  Choroidal perfusion and thickness both increase in response to systemic sildenafil. These changes could secondarily affect retinal function, explain previously reported clinical symptoms and potentially be a useful adjunct for treatment of ocular diseases that would benefit from increased choroidal blood flow.
Clinicopathological study of nasal polyps with special reference to mast cells in inflammatory polyps
Authors: Shulbha V. S. , Dayananda B. S.
Published: September 2012

Background and aim: Nasal polyposis is a relatively common condition found in 1–4% of the general population and in high percentages of some groups of patients. Nasal polyps diagnosed clinically are not always of inflammatory origin. A variety of non‐neoplastic and neoplastic conditions can present as nasal polyps. The aim of this study was to determine the various histopathological types, the predominant cells involved in the pathogenesis of inflammatory polyps with special reference to mast cells and to correlate them clinicopathologically. Methods: A total of 100 cases clinically diagnosed as nasal polyp, were studied over a period of 18 months. Results: Out of 100 cases studied, 91% of them were non‐neoplastic and 9% were neoplastic. Among the non‐neoplastic conditions, non‐allergic polyps accounted for 70% and allergic polyps accounted for 21% of cases. Among the neoplastic lesions, 6% were benign and 3% malignant. Squamous metaplasia was seen in 16.38% of cases. In stroma, mononuclear cells were predominant in 63.7% of inflammatory polyps, eosinophils in 19.11%, prominent edematous stroma in 26.39%, and vasculature > 2/high power field (hpf) in 20.39% of inflammatory polyps. 0–5 mast cells per 10 hpf were seen in 97.8% of inflammatory polyps in epithelium, whereas 11–20 mast cells in 26.4% of inflammatory polyps were seen in stroma. Conclusions: Nasal polyps diagnosed clinically are not always of inflammatory origin and therefore have to be subjected for histopathology.
The Effects of Strategy–Management Control System Misfits on Firm Performance
Authors: Gani Lindawati , Jermias Johnny
Published: September 2012

The purpose of this study is to investigate the effects of misfits between business strategy and management control systems on performance. We address the following research question: Do firms that align their management control systems with the specific requirements of their business strategy perform significantly better than those that do not achieve the required match? We define a misfit as the degree to which management control systems deviate from empirically derived optimal configurations for a given type of business strategy. We use the two‐stage approach proposed by Ittner and Larcker (2001) to measure misfit and to investigate the impacts of misfit on performance. Based on a questionnaire survey of executives from 109 banks, we hypothesize and find that the strategy–control systems misfit has a significantly negative correlation with both self‐rated and publicly available performance measures.
Hydroxypropylmethylcellulose films for the ophthalmic delivery of diclofenac sodium
Authors: El-Sousi Salah , Nácher Amparo , Mura Carla , Catalán-Latorre Ana , Merino Virginia , Merino-Sanjuán Matilde , Díez-Sales Octavio
Published: September 2012

Objectives

The aim of this study was to prepare diclofenac/hydroxypropylmethylcellulose (HPMC) and diclofenac-loaded nanoparticles/HPMC films as potential systems for ocular delivery.

Methods

Two different concentration of the polymer were used: 1.5 and 2.0% w/v. Chitosan–hyaluronic acid nanoparticles were prepared by the ionotropic gelation technique. Nanoparticles were characterized by transmission electron microscopy, dynamic light scattering, drug encapsulation efficiency and rheological studies. In-vitro drug studies and corneal penetration release studies were carried out. Drug release mechanism was finally evaluated by fitting the Ritger and Peppas equation to data. In addition corneal hydration level was calculated to determine whether films could damage the corneas.

Key findings

Diclofenac HPMC films presented a faster drug release and a higher drug penetration than nanoparticles; on the contrary nanoparticles containing films were able to give a more sustained release of the drug and thus a slower diclofenac permeation through the cornea than HPMC films.

Conclusions

Nanoparticles loaded with diclofenac sodium in HPMC films may be a valuable alternative for the treatment of ocular inflammatory diseases, since these formulations offer the benefit of sustained releasing directly to the site of action.
Characterization of Thielaviopsis paradoxa Isolates from Oil Palms in Colombia, Ecuador and Brazil
Authors: Álvarez Elizabeth , Llano Germán A. , Loke John B. , Chacon Maria I.
Published: September 2012

Ceratocystis paradoxa (Anamorph: Thielaviopsis paradoxa) is parasitic on a range of economic and food crops and is the cause of dry basal rot, a limiting disease in oil palm. The objective of this study was to determinate the pathogenic and genetic diversity of Thielaviopsis isolates from oil palms in Colombia, Ecuador and Brazil. A total of 164 strains of Thielaviopsis paradoxa were characterized using pathogenicity tests, random amplified polymorphic DNA (RAPD) markers and PCR sequencing of the internal transcribed spacer (ITS) region of 5.8 S ribosomal DNA. Oil palm seedlings were inoculated by injecting the base of stems in the seedling stage with a fungal suspension and severity scores of disease reactions were evaluated. PCR amplification of the ITS region resulted in a 590 base pair (bp) product. Digestion of the PCR product with two restriction enzymes produced three restriction patterns, which according to ITS sequences could be classified as T. paradoxa. Six RAPD primers gave polymorphic bands in T. paradoxa. Population structure analyses of the RAPD data suggested that most of the isolates obtained in this study belonged to a single population. The genetic diversity of the isolates from South America was intermediate, and therefore, T. paradoxa is likely to be predominantly clonal compared with Ceratocystis species. Sporadic sexual reproduction may occur for T. paradoxa but is secondary to clonal reproduction. Data on pathogen diversity will provide information on breeding strategies and population structures.
Characteristics of intrahepatic cholangiocarcinoma in patients with hepatitis B virus infection: clinicopathologic study of resected tumours
Authors: Wu Z.‐F. , Yang N. , Li D.‐Y. , Zhang H.‐B. , Yang G.‐S.
Published: September 2012

Recent efforts suggest an aetiological role of hepatitis B virus (HBV) infection in intrahepatic cholangiocarcinoma (ICC). The purpose of this study was to clarify the clinicopathologic characteristics and surgical outcomes of patients with HBV‐associated ICC. All patients with chronic HBV infection were identified from a database of patients with ICC that underwent surgical resection between 1 January 2005 and 31 December 2006. Their clinicopathologic and survival characteristics were compared with ICC patients without chronic HBV infection. The age of the HBV‐associated ICC patients tend to be younger than that of ICC patients without chronic HBV infection. HBV‐associated ICC patients tend to have higher abnormal α‐fetoprotein levels and lower abnormal serum carbohydrate antigen19‐9 (CA19‐9), r‐glutamyltransferase (r‐GT) and alkaline phosphatase levels. The pathologic features of the resected specimens revealed that HBV‐associated ICC patients tended to be of the mass‐forming type have a lower prevalence of lymphatic involvement and poorer tumour differentiation, and a higher prevalence of capsule formation and liver cirrhosis. Patients with HBV‐associated ICC had a significantly better survival than patients without chronic HBV infection. The clinicopathological features of HBV‐associated ICC patients showed significant differences from ICC patients without HBV infection. These tumours are characterized by the mass‐forming growth pattern and appeared to have a more favourable prognosis.
Characterization of the velvet regulators in Aspergillus fumigatus
Authors: Park Hee‐Soo , Bayram Özgür , Braus Gerhard H. , Kim Sun Chang , Yu Jae‐Hyuk
Published: September 2012

Fungal development and secondary metabolism is intimately associated via activities of the fungi‐specific velvet family proteins. Here we characterize the four velvet regulators in the opportunistic human pathogen Aspergillus fumigatus. The deletion of AfuvosA, AfuveA and AfuvelB causes hyperactive asexual development (conidiation) and precocious and elevated accumulation of AfubrlA during developmental progression. Moreover, the absence of AfuvosA, AfuveA or AfuvelB results in the abundant formation of conidiophores and highly increased AfubrlA mRNA accumulation in liquid submerged culture, suggesting that they act as repressors of conidiation. The deletion of AfuvosA or AfuvelB causes a reduction in conidial trehalose amount, long‐term spore viability, conidial tolerance to oxidative and UV stresses, and accelerated and elevated conidial germination regardless of the presence or absence of an external carbon source, suggesting an interdependent role of them in many aspects of fungal biology. Genetic studies suggest that AfuAbaA activates AfuvosA and AfuvelB expression during the mid to late phase of conidiation. Finally, the AfuveA null mutation can be fully complemented by Aspergillus nidulans VeA, which can physically interact with AfuVelB and AfuLaeA in vivo. A model depicting the similar yet different roles of the velvet regulators governing conidiation and sporogenesis in A. fumigatus is presented.
The basic chromospheres of skin that might not be differentiated visually: observations on aneurysmal fibrous histiocytomas and malignant melanomas
Authors: Oh Ga Na , Kim Jong Yeob , Choi Jae Eun , Seo Soo Hong , Kye Young Chul , Ahn Hyo Hyun
Published: September 2012

Aim

Aneurysmal fibrous histiocytoma (AFH) is a variant of fibrous histiocytoma, which has a cleft‐like cavernous blood‐filled space in the tumor. It appears as a single reddish black tumor with variable levels of pain and size from its bleeding. And, it must be differentiated from other similar looking malignant conditions such as malignant melanoma. The visual mimicry of AFH to melanoma was raised by some careful dermatologists, but never be confirmed objectively by colorimetric analysis.

Materials, Subjects, and Methods

In this study, we simply analyzed conventionally photographed digital images of thirty‐seven cases of fibrous histiocytomas, including three AFH cases into colorimetrically useful color space, CIELAB, of which coordinates are L*, a*, and b* representing lightness, red to green, and yellow to blue axis, respectively. In addition, we also analyzed the clinical digital images of seven cases of malignant melanomas. Using statistical package, each coordinates of CIELAB were compared using Wilcoxon rank sum test between AFH and melanomas. The CIELAB coordinates of AFH and non‐aneurysmal fibrous histiocytomas were compared statistically as well.

Results

Comparing with banal fibrous histiocytomas, the colors of AFH showed significantly smaller a* and b* coordinates (P = 0.008, 0.008, respectively), which implies more green and blue hue of AFH lesion. Rather, they were more like melanomas (P = 0.2839, 0.2040, respectively). As for L*, there were no significant differences for all comparisons.

Conclusions

As a result, more objective analysis of the digital images using colorimetric color space confirmed the visual mimicry of AFH to melanoma.
The late steps of plant nonsense‐mediated mRNA decay
Authors: Mérai Zsuzsanna , Benkovics Anna H. , Nyikó Tünde , Debreczeny Mónika , Hiripi László , Kerényi Zoltán , Kondorosi Éva , Silhavy Dániel
Published: September 2012

Nonsense‐mediated mRNA decay (NMD) is a eukaryotic quality control system that identifies and degrades mRNAs containing premature termination codons (PTCs). If translation terminates at a PTC, the UPF1 NMD factor binds the terminating ribosome and recruits UPF2 and UPF3 to form a functional NMD complex, which triggers the rapid decay of the PTC‐containing transcript. Although NMD deficiency is seedling lethal in plants, the mechanism of plant NMD remains poorly understood. To understand how the formation of the NMD complex leads to transcript decay we functionally mapped the UPF1 and SMG7 plant NMD factors, the putative key players of NMD target degradation. Our data indicate that the cysteine–histidine‐rich (CH) and helicase domains of UPF1 are only essential for the early steps of NMD, whereas the heavily phosphorylated N‐ and C–terminal regions play a redundant but essential role in the target transcript degradation steps of NMD. We also show that both the N‐ and the C–terminal regions of SMG7 are essential for NMD. The N terminus contains a phosphoserine‐binding domain that is required for the early steps of NMD, whereas the C terminus is required to trigger the degradation of NMD target transcripts. Moreover, SMG7 is a P–body component that can also remobilize UPF1 from the cytoplasm into processing bodies (P bodies). We propose that the N‐ and C–terminal phosphorylated regions of UPF1 recruit SMG7 to the functional NMD complex, and then SMG7 transports the PTC‐containing transcripts into P bodies for degradation.
Replication factor C1 (RFC1) is required for double‐strand break repair during meiotic homologous recombination in Arabidopsis
Authors: Liu Yang , Deng Yingtian , Li Gang , Zhao Jie
Published: September 2012

Replication factor C1 (RFC1), which is conserved in eukaryotes, is involved in DNA replication and checkpoint control. However, a RFC1 product participating in DNA repair at meiosis has not been reported in Arabidopsis. Here, we report functional characterization of AtRFC1 through analysis of the rfc1–2 mutant. The rfc1–2 mutant displayed normal vegetative growth but showed silique sterility because the male gametophyte was arrested at the uninucleus microspore stage and the female at the functional megaspore stage. Expression of AtRFC1 was concentrated in the reproductive organ primordia, meiocytes and developing gametes. Chromosome spreads showed that pairing and synapsis were normal, and the chromosomes were broken when desynapsis began at late prophase I, and chromosome fragments remained in the subsequent stages. For this reason, homologous chromosomes and sister chromatids segregated unequally, leading to pollen sterility. Immunolocalization revealed that the AtRFC1 protein localized to the chromosomes during zygotene and pachytene in wild‐type but were absent in the spo11–1 mutant. The chromosome fragmentation of rfc1–2 was suppressed by spo11–1, indicating that AtRFC1 acted downstream of AtSPO11‐1. The similar chromosome behavior of rad51 rfc1–2 and rad51 suggests that AtRFC1 may act with AtRAD51 in the same pathway. In summary, AtRFC1 is required for DNA double‐strand break repair during meiotic homologous recombination of Arabidopsis.
Mixed Mucosal Leishmaniasis Infection Caused by Leishmania tropica and Leishmania major
Authors: Shirian Sadegh , Oryan Ahmad , Hatam Gholam Reza , Daneshbod Yahya
Published: September 2012

Mixed infections with different
Leishmania
species could explain differences in the clinical courses of these infections. On identification of
Leishmania
parasites from Iranian patients with mucosal leishmaniasis (ML), a patient with both oral and nasal lesions was found to be concomitantly infected with
Leishmania tropica
and
L. major
. Mixed infection was identified by PCR amplification of
Leishmania
kinetoplast DNA on scraping of cytological smears and histopathological sections.
L. major
and
L. tropica
were isolated from the nasal and oral lesions, respectively. These species were also confirmed by immunohistochemistry. This seems to be the first reported case of concurrent ML infection with two
Leishmania
species. It indicates that, at least in this patient, previous infection with one of these
Leishmania
species did not protect against infection with the other. This result has important implications for the development of vaccines against leishmaniases and implies careful attention in the treatment of this infectious disease.
Performance Characteristics of the Cepheid Xpert
vanA
Assay for Rapid Identification of Patients at High Risk for Carriage of Vancomycin-Resistant Enterococci
Authors: Babady N. Esther , Gilhuley Kathleen , Cianciminio-Bordelon Diane , Tang Yi-Wei
Published: September 2012

We compared the performance characteristics of culture and the Cepheid Xpert
vanA
assay for routine surveillance of vancomycin-resistant enterococci (VRE) from rectal swabs in patients at high risk for VRE carriage. The Cepheid Xpert
vanA
assay had a limit of detection of 100 CFU/ml and correctly detected 101 well-characterized clinical VRE isolates with no cross-reactivity in 27 non-VRE and related culture isolates. The clinical sensitivity, specificity, positive predictive value, and negative predictive value of the Xpert
vanA
PCR assay were 100%, 96.9%, 91.3%, and 100%, respectively, when tested on 300 consecutively collected rectal swabs. This assay provides excellent predictive values for prompt identification of VRE-colonized patients in hospitals with relatively high rates of VRE carriage.
Enteroaggregative Escherichia coli O78:H10, the Cause of an Outbreak of Urinary Tract Infection
Authors: Olesen Bente , Scheutz Flemming , Andersen Rebecca L. , Menard Megan , Boisen Nadia , Johnston Brian , Hansen Dennis S. , Krogfelt Karen A. , Nataro James P. , Johnson James R.
Published: September 2012

In 1991, multiresistant
Escherichia coli
O78:H10 strains caused an outbreak of urinary tract infections in Copenhagen, Denmark. The phylogenetic origin, clonal background, and virulence characteristics of the outbreak isolates, and their relationship to nonoutbreak O78:H10 strains according to these traits and resistance profiles, are unknown. Accordingly, we extensively characterized 51 archived
E. coli
O78:H10 isolates (48 human isolates from seven countries, including 19 Copenhagen outbreak isolates, and 1 each of calf, avian, and unknown-source isolates), collected from 1956 through 2000.
E. coli
O78:H10 was clonally heterogeneous, comprising one dominant clonal group (61% of isolates, including all 19 outbreak isolates) from ST10 (phylogenetic group A) plus several minor clonal groups (phylogenetic groups A and D). All ST10 isolates, versus 25% of non-ST10 isolates, were identified by molecular methods as enteroaggregative
E. coli
(EAEC) (
P
< 0.001). Genes present in >90% of outbreak isolates included
fimH
(type 1 fimbriae; ubiquitous in
E. coli
);
fyuA
,
traT
, and
iutA
(associated with extraintestinal pathogenic
E. coli
[ExPEC]); and
sat
,
pic
,
aatA
,
aggR
,
aggA
, ORF61,
aaiC
,
aap
, and ORF3 (associated with EAEC). An outbreak isolate was lethal in a murine subcutaneous sepsis model and exhibited characteristic EAEC “stacked brick” adherence to cultured epithelial cells. Thus, the 1991 Copenhagen outbreak was caused by a tight, non-animal-associated subset within a broadly disseminated O78:H10 clonal group (ST10; phylogenetic group A), members of which exhibit both ExPEC and EAEC characteristics, whereas O78:H10 isolates overall are phylogenetically diverse. Whether ST10 O78:H10 EAEC strains are both uropathogenic and diarrheagenic warrants further investigation.
The Diagnostic Performance of the GenoType MTBDR
plus
Version 2 Line Probe Assay Is Equivalent to That of the Xpert MTB/RIF Assay
Authors: Barnard M. , Gey van Pittius N. C. , van Helden P. D. , Bosman M. , Coetzee G. , Warren R. M.
Published: September 2012

Molecular diagnostics for
Mycobacterium tuberculosis
have recently been endorsed by the World Health Organization. The Xpert MTB/RIF assay was endorsed for use on patient material, regardless of smear gradation, while the GenoType MTBDR
plus
(version 1) has been limited for use on smear-positive patient material. In this study, we evaluated the diagnostic performance of the Xpert MTB/RIF and GenoType MTBDR
plus
(version 2) assays on smear-positive and smear-negative patient specimens submitted to a high-throughput diagnostic laboratory. A total of 282 consecutive specimens were subjected to the two new molecular assays, and their performance characteristics were assessed relative to the routine diagnostic standard. Both assays showed similar diagnostic performance characteristics. The sensitivities of the GenoType MTBDR
plus
(v2.0) and Xpert MTB/RIF assays for the detection of culture-positive
M. tuberculosis
were 73.1% and 71.2%, respectively, while the specificities of both assays were 100%. Both assays were able to diagnose the presence of
M. tuberculosis
in 57 to 58% of smear-negative cases, suggesting that the performance characteristics were dependent on bacillary load. The detection of
M. tuberculosis
in culture-negative specimens confirmed that molecular assays should not be used for treatment monitoring. The sensitivity and specificity for rifampin resistance detection were 100% in both assays; however, the GenoType MTBDR
plus
(v2.0) assay provided additional information on isoniazid susceptibility. The GenoType MTBDR
plus
(v2.0) assay will complement the Xpert MTB/RIF screening assay by validating rifampin susceptibility and providing information on isoniazid susceptibility. In addition, the GenoType MTBDR
plus
(v2.0) assay will provide pharmacogenetic information that may be critical in guiding appropriate treatment.
Deletion of Specific Immune-Modulatory Genes from Modified Vaccinia Virus Ankara-Based HIV Vaccines Engenders Improved Immunogenicity in Rhesus Macaques
Authors: Garber David A. , O'Mara Leigh A. , Gangadhara Sailaja , McQuoid Monica , Zhang Xiugen , Zheng Rui , Gill Kiran , Verma Meena , Yu Tianwei , Johnson Brent , Li Bing , Derdeyn Cynthia A. , Ibegbu Chris , Altman John D. , Hunter Eric , Feinberg Mark B.
Published: September 2012

Modified vaccinia virus Ankara (MVA) is a safe, attenuated orthopoxvirus that is being developed as a vaccine vector but has demonstrated limited immunogenicity in several early-phase clinical trials. Our objective was to rationally improve the immunogenicity of MVA-based HIV/AIDS vaccines via the targeted deletion of specific poxvirus immune-modulatory genes. Vaccines expressing codon-optimized HIV subtype C consensus Env and Gag antigens were generated from MVA vector backbones that (i) harbor simultaneous deletions of four viral immune-modulatory genes, encoding an interleukin-18 (IL-18) binding protein, an IL-1β receptor, a dominant negative Toll/IL-1 signaling adapter, and CC-chemokine binding protein (MVAΔ4-HIV); (ii) harbor a deletion of an additional (fifth) viral gene, encoding uracil-DNA glycosylase (MVAΔ5-HIV); or (iii) represent the parental MVA backbone as a control (MVA-HIV). We performed head-to-head comparisons of the cellular and humoral immune responses that were elicited by these vectors during homologous prime-boost immunization regimens utilizing either high-dose (2 × 10
8
PFU) or low-dose (1 × 10
7
PFU) intramuscular immunization of rhesus macaques. At all time points, a majority of the HIV-specific T cell responses, elicited by all vectors, were directed against Env, rather than Gag, determinants, as previously observed with other vector systems. Both modified vectors elicited up to 6-fold-higher frequencies of HIV-specific CD8 and CD4 T cell responses and up to 25-fold-higher titers of Env (gp120)-specific binding (nonneutralizing) antibody responses that were relatively transient in nature. While the correlates of protection against HIV infection remain incompletely defined, our results indicate that the rational deletion of specific genes from MVA vectors can positively alter their cellular and humoral immunogenicity profiles in nonhuman primates.
The NS1 Protein of Influenza A Virus Interacts with Cellular Processing Bodies and Stress Granules through RNA-Associated Protein 55 (RAP55) during Virus Infection
Authors: Mok Bobo Wing-Yee , Song Wenjun , Wang Pui , Tai Hung , Chen Yixin , Zheng Min , Wen Xi , Lau Siu-Ying , Wu Wai Lan , Matsumoto Ken , Yuen Kwok-Yung , Chen Honglin
Published: September 2012

The nonstructural protein (NS1) of influenza A virus performs multiple functions in the virus life cycle. Proteomic screening for cellular proteins which interact with NS1 identified the cellular protein RAP55, which is one of the components of cellular processing bodies (P-bodies) and stress granules. To verify whether NS1 interacts with cellular P-bodies, interactions between NS1, RAP55, and other P-body-associated proteins (Ago1, Ago2, and DCP1a) were confirmed using coimmunoprecipitation and cellular colocalization assays. Overexpression of RAP55 induced RAP55-associated stress granule formation and suppressed virus replication. Knockdown of RAP55 with small interfering RNA (siRNA) or expression of a dominant-negative mutant RAP55 protein with defective interaction with P-bodies blocked NS1 colocalization to P-bodies in cells. Expression of NS1 inhibited RAP55 expression and formation of RAP55-associated P-bodies/stress granules. The viral nucleoprotein (NP) was found to be targeted to stress granules in the absence of NS1 but localized to P-bodies when NS1 was coexpressed. Restriction of virus replication via P-bodies occurred in the early phases of infection, as the number of RAP55-associated P-bodies in cells diminished over the course of virus infection. NS1 interaction with RAP55-associated P-bodies/stress granules was associated with RNA binding and mediated via a protein kinase R (PKR)-interacting viral element. Mutations introduced into either RNA binding sites (R38 and K41) or PKR interaction sites (I123, M124, K126, and N127) caused NS1 proteins to lose the ability to interact with RAP55 and to inhibit stress granules. These results reveal an interplay between virus and host during virus replication in which NP is targeted to P-bodies/stress granules while NS1 counteracts this host restriction mechanism.
Incorporation of Host Complement Regulatory Proteins into Newcastle Disease Virus Enhances Complement Evasion
Authors: Biswas Moanaro , Johnson John B. , Kumar Sandeep R. P. , Parks Griffith D. , Subbiah Elankumaran
Published: September 2012

Newcastle disease virus (NDV), an avian paramyxovirus, is inherently tumor selective and is currently being considered as a clinical oncolytic virus and vaccine vector. In this study, we analyzed the effect of complement on the neutralization of NDV purified from embryonated chicken eggs, a common source for virus production. Fresh normal human serum (NHS) neutralized NDV by multiple pathways of complement activation, independent of neutralizing antibodies. Neutralization was associated with C3 deposition and the activation of C2, C3, C4, and C5 components. Interestingly, NDV grown in mammalian cell lines was resistant to complement neutralization by NHS. To confirm whether the incorporation of regulators of complement activity (RCA) into the viral envelope afforded complement resistance, we grew NDV in CHO cells stably transfected with CD46 or HeLa cells, which strongly express CD46 and CD55. NDV grown in RCA-expressing cells was resistant to complement by incorporating CD46 and CD55 on virions. Mammalian CD46 and CD55 molecules on virions exhibited homologous restriction, since chicken sera devoid of neutralizing antibodies to NDV were able to effectively neutralize these virions. The incorporation of chicken RCA into NDV produced in embryonated eggs similarly provided species specificity toward chicken sera.
Differential Clade-Specific HLA-B*3501 Association with HIV-1 Disease Outcome Is Linked to Immunogenicity of a Single Gag Epitope
Authors: Matthews Philippa C. , Koyanagi Madoka , Kløverpris Henrik N. , Harndahl Mikkel , Stryhn Anette , Akahoshi Tomohiro , Gatanaga Hiroyuki , Oka Shinichi , Juarez Molina Claudia , Valenzuela Ponce Humberto , Avila Rios Santiago , Cole David , Carlson Jonathan , Payne Rebecca P. , Ogwu Anthony , Bere Alfred , Ndung'u Thumbi , Gounder Kamini , Chen Fabian , Riddell Lynn , Luzzi Graz , Shapiro Roger , Brander Christian , Walker Bruce , Sewell Andrew K. , Reyes Teran Gustavo , Heckerman David , Hunter Eric , Buus Søren , Takiguchi Masafumi , Goulder Philip J. R.
Published: September 2012

The strongest genetic influence on immune control in HIV-1 infection is the HLA class I genotype. Rapid disease progression in B-clade infection has been linked to HLA-B*35 expression, in particular to the less common HLA-B*3502 and HLA-B*3503 subtypes but also to the most prevalent subtype, HLA-B*3501. In these studies we first demonstrated that whereas HLA-B*3501 is associated with a high viral set point in two further B-clade-infected cohorts, in Japan and Mexico, this association does not hold in two large C-clade-infected African cohorts. We tested the hypothesis that clade-specific differences in HLA associations with disease outcomes may be related to distinct targeting of critical CD8+T-cell epitopes. We observed that only one epitope was significantly targeted differentially, namely, the Gag-specific epitope NPPIPVGDIY (NY10, Gag positions 253 to 262) (P= 2 × 10−5). In common with two other HLA-B*3501-restricted epitopes, in Gag and Nef, that were not targeted differentially, a response toward NY10 was associated with a significantly lower viral set point. Nonimmunogenicity of NY10 in B-clade-infected subjects derives from the Gag-D260E polymorphism present in ∼90% of B-clade sequences, which critically reduces recognition of the Gag NY10 epitope. These data suggest that in spite of any inherent HLA-linked T-cell receptor repertoire differences that may exist, maximizing the breadth of the Gag-specific CD8+T-cell response, by the addition of even a single epitope, may be of overriding importance in achieving immune control of HIV infection. This distinction is of direct relevance to development of vaccines designed to optimize the anti-HIV CD8+T-cell response in all individuals, irrespective of HLA type.
MicroRNAs and Unusual Small RNAs Discovered in Kaposi's Sarcoma-Associated Herpesvirus Virions
Authors: Lin Xianzhi , Li Xiaofan , Liang Deguang , Lan Ke
Published: September 2012

It is widely held that any given virus uses only one type of nucleic acid for genetic information storage. However, this consensus has been challenged slightly by several recent studies showing that many RNA species are present within a range of DNA viruses that include Kaposi's sarcoma-associated herpesvirus (KSHV). RNAs extracted from purified DNA virus particles exhibit great diversity in terms of length, abundance, temporal expression, cellular localization, and coding capacity during viral infection. In addition to known RNA species, the current study showed that small regulatory RNAs were present in KSHV virions. A large number of viral and cellular microRNAs (miRNAs), as well as unusual small RNAs (usRNAs), were detected in KSHV virions by using deep sequencing. Both viral and host miRNAs detected in small RNAs extracted from KSHV virions were further shown to colocalize with KSHV virions directly by
in situ
hybridization (ISH)-electron microscopy (EM) (ISH-EM). Some of these miRNAs were differentially present in the host cells and KSHV virions, suggesting that they are not randomly present in KSHV virions. The virional miRNAs could be transported into host cells, and they are biologically functional during
de novo
viral infection. Our study revealed miRNAs and usRNAs as a novel group of components in KSHV virions.
Essential Cell-Autonomous Role for Interferon (IFN) Regulatory Factor 1 in IFN-γ-Mediated Inhibition of Norovirus Replication in Macrophages
Authors: Maloney Nicole S. , Thackray Larissa B. , Goel Gautam , Hwang Seungmin , Duan Erning , Vachharajani Punit , Xavier Ramnik , Virgin Herbert W.
Published: September 2012

Noroviruses (NVs) cause the majority of cases of epidemic nonbacterial gastroenteritis worldwide and contribute to endemic enteric disease. However, the molecular mechanisms responsible for immune control of their replication are not completely understood. Here we report that the transcription factor interferon regulatory factor 1 (IRF-1) is required for control of murine NV (MNV) replication and pathogenesis
in vivo
. This led us to studies documenting a cell-autonomous role for IRF-1 in gamma interferon (IFN-γ)-mediated inhibition of MNV replication in primary macrophages. This role of IRF-1 in the inhibition of MNV replication by IFN-γ is independent of IFN-αβ signaling. While the signal transducer and activator of transcription STAT-1 was also required for IFN-γ-mediated inhibition of MNV replication
in vitro
, class II transactivator (CIITA), interferon regulatory factor 3 (IRF-3), and interferon regulatory factor 7 (IRF-7) were not required. We therefore hypothesized that there must be a subset of IFN-stimulated genes (ISGs) regulated by IFN-γ in a manner dependent only on STAT-1 and IRF-1. Analysis of transcriptional profiles of macrophages lacking various transcription factors confirmed this hypothesis. These studies identify a key role for IRF-1 in IFN-γ-dependent control of norovirus infection in mice and macrophages.
Long-Term Nonprogressor and Elite Controller Patients Who Control Viremia Have a Higher Percentage of Methylation in Their HIV-1 Proviral Promoters than Aviremic Patients Receiving Highly Active Antiretroviral Therapy
Authors: Palacios Juan Antonio , Pérez-Piñar Teresa , Toro Carlos , Sanz-Minguela Beatriz , Moreno Victoria , Valencia Eulalia , Gómez-Hernando César , Rodés Berta
Published: September 2012

Several factors are involved in the control of HIV transcription/replication, including epigenetic modifications at the promoter level. Analysis of the HIV long terminal repeat (LTR) methylation status in infected patients controlling viremia is scarce. Herein, we show a higher degree of DNA methylation in the 5′-LTR of long-term nonprogressor and elite controller (LTNP/EC) versus progressor patients and a positive correlation with time of infection, indicating a certain contribution of HIV LTR silencing in reducing the number of replicating viruses which may account for a delayed progression.