bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wetting layer evolution and its temperature dependence during self-assembly of InAs/GaAs quantum dots
Authors: Zhang Hongyi , Chen Yonghai , Zhou Guanyu , Tang Chenguang , Wang Zhanguo 
Published: October 2012

Abstract
For InAs/GaAs(001) quantum dot (QD) system, the wetting layer (WL) evolution and its temperature dependence were studied using reflectance difference spectroscopy and were analyzed with a rate equation model. WL thicknesses showed a monotonic increase at relatively low growth temperatures but showed an initial increase and then decrease at higher temperatures, which were unexpected from a thermodynamic understanding. By adopting a rate equation model, the temperature dependence of QD formation rate was assigned as the origin of different WL evolutions. A brief discussion on the indium desorption was given. Those results gave hints of the kinetic aspects of QD self-assembly.
Well-width dependence of the emission linewidth in ZnO/MgZnO quantum wells
Authors: Lv Xue-Qin , Zhang Jiang-Yong , Ying Lei-Ying , Liu Wen-Jie , Hu Xiao-Long , Zhang Bao-Ping , Qiu Zhi-Ren , Kuboya Shigeyuki , Onabe Kentaro 
Published: October 2012

Abstract
Photoluminescence (PL) spectra were measured as a function of well width (L
W) and temperature in ZnO/Mg0.1Zn0.9O single quantum wells (QWs) with graded thickness. The emission linewidth (full width at half maximum) was extracted from the emission spectra, and its variation as a function of L
W was studied. The inhomogeneous linewidth obtained at 5 K was found to decrease with increasing L
W from 1.8 to 3.3 nm due to the reduced potential variation caused by the L
W fluctuation. Above 3.3 nm, however, the linewidth became larger with increasing L
W, which was explained by the effect related with defect generation due to strain relaxation and exciton expansion in the QW. For the homogenous linewidth broadening, longitudinal optical (LO) phonon scattering and impurity scattering were taken into account. The LO phonon scattering coefficient Γ
LO and impurity scattering coefficient Γ
imp were deduced from the temperature dependence of the linewidth of the PL spectra. Evident reduction of Γ
LO with decreasing L
W was observed, which was ascribed to the confinement-induced enhancement of the exciton binding energy. Different from Γ
LO, a monotonic increase in Γ
imp was observed with decreasing L
W, which was attributed to the enhanced penetration of the exciton wave function into the barrier layers.
A distributed message in message aware concurrent transmission protocol in IEEE 802.11 WLANs
Authors: Kang Young-myoung , Yoo Joon , Lee Joonsoo , Kim Chong-kwon 
Published: October 2012

Abstract
The IEEE 802.11 distributed coordination function (DCF) employs the carrier sense technology to avoid frame collisions. However, recent measurement studies demonstrate that the physical layer (PHY) capture effect frequently occurs; even when frames collide, one of them can be decoded successfully if its relative signal strength is high enough. Furthermore, a new wireless PHY technology, called Message In Message (MIM), adopts an advanced preamble detection function to enhance the PHY capture effect. To fully exploit MIM in multi-collision environments, frame transmission orders have to be carefully scheduled. It also requires tight time synchronization at multiple access points (APs), thus induces large overheads. In this article, we propose an opportunistic concurrent transmission protocol called
D

istributed
O pportunistic M IM-aware C oncurrent T ransmission (DOMCT) which exploits the MIM functionality in a distributed manner obliterating the centralized control. In DOMCT, APs first prepare interference MAPs to discover the possible simultaneous MIM transmission opportunities. Detecting the inadvertent frame transmission from a neighboring AP, an AP transmits another frame intentionally if both frames can successfully be decoded at destination nodes by the MIM capture effect. Through both analysis and extensive ns-2 simulations, we show that DOMCT outperforms the legacy DCF by up to 61% and observe comparable performance to that of the centralized approach.
Layered multimedia broadcast using rateless codes with progressive recovery over cooperative MIMO
Authors: Chen Zhao , Yin Liuguo , Xu Mai , Lu Jianhua 
Published: October 2012

AbstractThis article proposes a novel scheme, based on unequal error protected rateless codes, for broadcasting layered multimedia over cooperative multiple-input multiple-output (MIMO). By taking advantage of both cooperation and broadcasting, we first present a two-phase cooperative MIMO broadcast scheme, which exploits distributed diversity in point-to-multipoint communication scenarios. Then, to enhance layered multimedia transmission with progressive recovery, the progressive rateless codes (PRC) is proposed to recover the layered data according to their importance at the expected received ratio of all output packets. Thus, receivers with different packet loss rate can achieve an adaptive recovery of the layered multimedia progressively. Furthermore, based on PRC, a distortion-based layered multimedia broadcast problem is formulated, which optimizes source bitrate of the layered multimedia and coding rates of PRC to improve the quality of experience (QoE) of the multimedia delivery over all receivers. The performance analysis including both analytical results and simulation experiments of Motion-JPEG 2000 broadcast to receivers verifies the superiority of the cooperative broadcast and efficiency of the QoE-driven optimization algorithm.
Targeted blockade in lethal West Nile virus encephalitis indicates a crucial role for very late antigen (VLA)-4-dependent recruitment of nitric oxide-producing macrophages
Authors: Getts Daniel R , Terry Rachael L , Getts Meghann Teague , Müller Marcus , Rana Sabita , Deffrasnes Celine , Ashhurst Thomas Myles , Radford Jane , Hofer Markus , Thomas Shane , Campbell Iain L , King Nicholas JC 
Published: October 2012

Abstract
Infiltration of Ly6Chi monocytes from the blood is a hallmark of viral encephalitis. In mice with lethal encephalitis caused by West Nile virus (WNV), an emerging neurotropic flavivirus, inhibition of Ly6Chi monocyte trafficking into the brain by anti-very late antigen (VLA)-4 integrin antibody blockade at the time of first weight loss and leukocyte influx resulted in long-term survival of up to 60% of infected mice, with subsequent sterilizing immunity. This treatment had no effect on viral titers but appeared to be due to inhibition of Ly6Chi macrophage immigration. Although macrophages isolated from the infected brain induced WNV-specific CD4+ T-cell proliferation, T cells did not directly contribute to pathology, but are likely to be important in viral control, as antibody-mediated T-cell depletion could not reproduce the therapeutic benefit of anti-VLA-4. Instead, 70% of infiltrating inflammatory monocyte-derived macrophages were found to be making nitric oxide (NO). Furthermore, aminoguanidine-mediated inhibition of induced NO synthase activity in infiltrating macrophages significantly prolonged survival, indicating involvement of NO in the immunopathology. These data show for the first time the therapeutic effects of temporally targeting pathogenic NO-producing macrophages during neurotropic viral encephalitis.
Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome
Authors: Song Hongshuo , Pavlicek Jeffrey W , Cai Fangping , Bhattacharya Tanmoy , Li Hui , Iyer Shilpa S , Bar Katharine J , Decker Julie M , Goonetilleke Nilu , Liu Michael KP , Berg Anna , Hora Bhavna , Drinker Mark S , Eudailey Josh , Pickeral Joy , Moody M Anthony , Ferrari Guido , McMichael Andrew , Perelson Alan S , Shaw George M , Hahn Beatrice H , Haynes Barton F , Gao Feng 
Published: October 2012

Abstract

Background
A modest change in HIV-1 fitness can have a significant impact on viral quasispecies evolution and viral pathogenesis, transmission and disease progression. To determine the impact of immune escape mutations selected by cytotoxic T lymphocytes (CTL) on viral fitness in the context of the cognate transmitted/founder (T/F) genome, we developed a new competitive fitness assay using molecular clones of T/F genomes lacking exogenous genetic markers and a highly sensitive and precise parallel allele-specific sequencing (PASS) method.

Results
The T/F and mutant viruses were competed in CD4+ T-cell enriched cultures, relative proportions of viruses were assayed after repeated cell-free passage, and fitness costs were estimated by mathematical modeling. Naturally occurring HLA B57-restricted mutations involving the TW10 epitope in Gag and two epitopes in Tat/Rev and Env were assessed independently and together. Compensatory mutations which restored viral replication fitness were also assessed. A principal TW10 escape mutation, T242N, led to a 42% reduction in replication fitness but V247I and G248A mutations in the same epitope restored fitness to wild-type levels. No fitness difference was observed between the T/F and a naturally selected variant carrying the early CTL escape mutation (R355K) in Env and a reversion mutation in the Tat/Rev overlapping region.

Conclusions
These findings reveal a broad spectrum of fitness costs to CTL escape mutations in T/F viral genomes, similar to recent findings reported for neutralizing antibody escape mutations, and highlight the extraordinary plasticity and adaptive potential of the HIV-1 genome. Analysis of T/F genomes and their evolved progeny is a powerful approach for assessing the impact of composite mutational events on viral fitness.
Identification of novel CDK9 and Cyclin T1-associated protein complexes (CCAPs) whose siRNA depletion enhances HIV-1 Tat function
Authors: Ramakrishnan Rajesh , Liu Hongbing , Donahue Hart , Malovannaya Anna , Qin Jun , Rice Andrew P 
Published: October 2012

AbstractBackgroundHIV-1 Tat activates RNA Polymerase II (RNAP II) elongation of the integrated provirus by recruiting a protein kinase known as P-TEFb to TAR RNA at the 5′end of nascent viral transcripts. The catalytic core of P-TEFb contains CDK9 and Cyclin T1 (CCNT1). A human endogenous complexome has recently been described – the set of multi-protein complexes in HeLa cell nuclei. We mined this complexome data set and identified 12 distinct multi-protein complexes that contain both CDK9 and CCNT1. We have termed these complexes CCAPs forCDK9/CCNT1-associatedprotein complexes. Nine CCAPs are novel, while three were previously identified as Core P-TEFb, the 7SK snRNP, and the Super-Elongation Complex. We have investigated the role of five newly identified CCAPs in Tat function and viral gene expression.ResultsWe examined five CCAPs that contain: 1) PPP1R10/TOX3/WDR82; 2) TTF2; 3) TPR; 4) WRNIP1; 5) FBXO11/CUL1/SKP1. SiRNA depletions of protein subunits of the five CCAPs enhanced Tat activation of an integrated HIV-1 LTR-Luciferase reporter in TZM-bl cells. Using plasmid transfection assays in HeLa cells, we also found that siRNA depletions of TTF2, FBXO11, PPP1R10, WDR82, and TOX3 enhanced Tat activation of an HIV-1 LTR-luciferase reporter, but the depletions did not enhance expression of an NF-κB reporter plasmid with the exception of PPP1R10. We found no evidence that depletion of CCAPs perturbed the level of CDK9/CCNT1 in the 7SK snRNP. We also found that the combination of siRNA depletions of both TTF2 and FBXO11 sensitized a latent provirus in Jurkat cells to reactivation by sub-optimal amounts of αCD3/CD28 antibodies.ConclusionsOur results identified five novel CDK9/CCNT1 complexes that are capable of negative regulation of HIV-1 Tat function and viral gene expression. Because siRNA depletions of CCAPs enhance Tat function, it is possible that these complexes reduce the level of CDK9 and CCNT1 available for Tat, similar to the negative regulation of Tat by the 7SK snRNP. Our results highlight the complexity in the biological functions of CDK9 and CCNT1.
An improved respiratory syncytial virus neutralization assay based on the detection of green fluorescent protein expression and automated plaque counting
Authors: van Remmerden Yvonne , Xu Fang , van Eldik Mandy , Heldens Jacco GM , Huisman Willem , Widjojoatmodjo Myra N 
Published: October 2012

Abstract

Background
Virus neutralizing antibodies against respiratory syncytial virus (RSV) are considered important correlates of protection for vaccine evaluation. The established plaque reduction assay is time consuming, labor intensive and highly variable.

Methods
Here, a neutralization assay based on a modified RSV strain expressing the green fluorescent protein in combination with automated detection and quantification of plaques is described.

Results
The fluorescence plaque reduction assay in microplate format requires only two days to complete and is simple and reproducible. A good correlation between visual and automated counting methods to determine RSV neutralizing serum antibody titers was observed.

Conclusions
The developed virus neutralization assay is suitable for high-throughput testing and can be used for both animal studies and (large scale) vaccine clinical trials.
Acute risk for hepatitis E virus infection among HIV-1-positive pregnant women in central Africa
Authors: Caron Mélanie , Bouscaillou Julie , Kazanji Mirdad 
Published: October 2012

Abstract

Background
Hepatitis E virus (HEV), an enterically transmitted pathogen, is highly endemic in several African countries. Pregnant women are at particularly high risk for acute or severe hepatitis E. In Gabon, a central African country, the prevalence of antibodies to HEV among pregnant women is 14.1%. Recent studies have demonstrated unusual patterns of hepatitis E (chronic hepatitis, cirrhosis) among immunodeficient patients.

Findings
We investigated the prevalence of antibodies to HEV among pregnant women infected with HIV-1 or HTLV-1 in Gabon. Of 243 samples collected, 183 were positive for HIV-1 and 60 for HTLV-1; 16 women (6.6%) had IgG antibodies to HEV. The seroprevalence was higher among HIV-1-infected women (7.1%) than HTLV-1-infected women (5.0%). Moreover, the HIV-1 viral load was significantly increased (p ≤ 0.02) among women with past-HEV exposure (1.3E+05 vs 5.7E+04 copies per ml), whereas no difference was found in HTLV-1 proviral load (9.0E+01 vs 1.1E+03 copies per ml).

Conclusions
These data provide evidence that HIV-1-infected women are at risk for acute or severe infection if they are exposed to HEV during pregnancy, with an increased viral load.
Human Papillomavirus (HPV) genotype 18 variants in patients with clinical manifestations of HPV related infections in Bilbao, Spain
Authors: Arroyo Sara L , Basaras Miren , Arrese Elixabete , Hernáez Silvia , Andía Daniel , Esteban Valentín , Garcia-Etxebarria Koldo , Jugo Begoña M , Cisterna Ramón 
Published: November 2012

Abstract

Background
Human papillomavirus (HPV) variants differ in their biological and chemical properties, and therefore, may present differences in pathogenicity. Most authors classified variants based on the phylogenetic analysis of L1 region. Nevertheless, recombination in HPV samples is becoming a usual finding and thus, characterizing genetic variability in other regions should be essential.

Objectives
We aimed to characterize the genetic variability of HPV 18 in 5 genomic regions: E6, E7, E4, L1 and the Upstream Regulatory Region (URR), working with both single infection and multiple HPV infection samples. Furthermore, we aimed to assess the prevalence of HPV 18 variants in our region and look for possible existence of recombination as well as analyze the relationship between these variants and the type of lesion.

Methods
From 2007 to 2010, Clinical Microbiology and Infection Control Department analyzed 44 samples which were positive for HPV 18. Genetic variability was determined in PCR products and variants were assigned to European, Asian-amerindian or African lineage. Recombination and association of variants with different types of lesion was studied.

Results
Genetic analysis of the regions revealed a total of 56 nucleotide variations. European, African and Asian-amerindian variants were found in 25/44 (56.8%), 10/44 (22.7%) and 5/44 (11.4%) samples, respectively. We detected the presence of recombinant variants in 2/44 (4.5%) cases. Samples taken from high-grade squamous intraepithelial lesions (H-SIL) only presented variants with specific-african substitutions.

Conclusions
Multiple HPV infection, non-european HPV variants prevalence and existence of recombination are considered risk factors for HPV persistence and progression of intraepithelial abnormalities, and therefore, should be taken into consideration in order to help to design and optimize diagnostics protocols as well as improve epidemiologic studies.
Our study is one of the few studies in Spain which analyses the genetic variability of HPV18 and we showed the importance of characterizing more than one genomic region in order to detect recombination and classify HPV variants properly.
Comparisons of the iron deficient metabolic response in rats fed either an AIN-76 or AIN-93 based diet
Authors: Davis McKale R , Hester Kristen K , Shawron Krista M , Lucas Edralin A , Smith Brenda J , Clarke Stephen L 
Published: October 2012

Abstract

Background
Previous studies examining the metabolic consequences of dietary iron deficiency have reported elevated serum glucose concentrations in iron-deficient animals. Importantly, the majority of these findings were observed using an earlier version of a laboratory animal diet (AIN-76A) in which the primary carbohydrate source was sucrose – a disaccharide known to negatively impact both glucose and lipid homeostasis. The AIN-76A diet formula was improved in 1993 (AIN-93) to optimize animal nutrition with a major change being the substitution of cornstarch for sucrose. Therefore, we sought to examine the effects of iron deficiency on steady-state glucose homeostasis and the hepatic expression of glucose- and lipid-related genes in rats fed an iron-deficient diet based on either an AIN-76A or AIN-93 diet.

Methods
The study design consisted of 6 treatment groups: control (C; 40 mg Fe/kg diet), iron deficient (ID; ≤ 3 mg Fe/kg diet), or pair-fed (PF; 40 mg Fe/kg) fed either an AIN-76A or AIN-93 diet for 21 d. Hemoglobin and hematocrit were measured in whole blood. Serum insulin and cortisol were measure by ELISA. Serum glucose and triacylglycerols were measured by standard colorimetric enzyme assays. Alterations in hepatic gene expression were determined by real-time qPCR.

Results
Hemoglobin and hematocrit were significantly reduced in both ID groups compared to the C and PF groups. Similarly, animals in the both ID groups exhibited elevated steady-state levels of blood glucose and insulin, and significantly decreased levels of circulating cortisol compared to their respective PF controls. Serum triacyglycerols were only increased in ID animals consuming the AIN-76A diet. Hepatic gene expression analyses revealed a ~4- and 3-fold increase in the expression of glucokinase and pyruvate dehydrogenase kinase-4 mRNA, respectively, in the ID group on either diet compared to their respective PF counterparts. In contrast, the expression of lipogenic genes was significantly elevated in the AIN-76 ID group, while expression of these genes was unaffected by iron status in the AIN-93 ID group.

Conclusions
These results indicate that an impaired iron status is sufficient to alter glucose homeostasis, though alterations in lipid metabolism associated with ID are only observed in animals receiving the AIN-76A diet.
Association of adipokines and adhesion molecules with indicators of obesity in women undergoing mammography screening
Authors: Isoppo de Souza Caroline , Rosa Daniela Dornelles , Ettrich Betina , Cibeira Gabriela Hermann , Giacomazzi Juliana , Tusset Paloma , Ashton-Prolla Patrícia , Medeiros Lidia Rosi , Caleffi Maira , Neto Eurico Camargo , Moriguchi Emilio Hideyuki , Graudenz Marcia Silveira 
Published: October 2012

Abstract

Background
The soluble cell adhesion molecules and adipokines are elevated in patients with obesity, hypertension, type 2 diabetes mellitus, breast cancer and atherosclerosis.

Objective
To investigate the relationship between anthropometric profile, dietary intake, lipid profile and fasting glycemia with serum levels of adipokines (adiponectin and PAI-1) and adhesion molecules (ICAM-1 and VCAM-1) in women without breast cancer undergoing routine mammographic screening.

Design
Transversal study.

Subjects
One hundred and forty-five women over 40-years old participated in this study.

Results
In 39.3% of cases the BMI was above 30 kg/m2; 46.9% had hypertension, 14.5% had type 2 Diabetes Mellitus, 31.7% had dyslipidemia and 88.3% presented a waist-to-hip ratio ≥ 0.8. A linear correlation was found between serum levels of PAI-1 and triglycerides, between serum levels of PAI-1 and WHR and between serum levels of VCAM-1 and BMI.

Conclusion
We found a high prevalence of obesity and metabolic syndrome. PAI-1 and VCAM-1 levels were correlated with clinical indicators of obesity and overweight.
Improvement in coronary heart disease risk factors during an intermittent fasting/calorie restriction regimen: Relationship to adipokine modulations
Authors: Kroeger Cynthia M , Klempel Monica C , Bhutani Surabhi , Trepanowski John F , Tangney Christine C , Varady Krista A 
Published: October 2012

Abstract

Background
The ability of an intermittent fasting (IF)-calorie restriction (CR) regimen (with or without liquid meals) to modulate adipokines in a way that is protective against coronary heart disease (CHD) has yet to be tested.

Objective
Accordingly, we examined the effects of an IFCR diet on adipokine profile, body composition, and markers of CHD risk in obese women.

Methods
Subjects (n = 54) were randomized to either the IFCR-liquid (IFCR-L) or IFCR-food based (IFCR-F) diet for 10 weeks.

Results
Greater decreases in body weight and waist circumference were noted in the IFCR-L group (4 ± 1 kg; 6 ± 1 cm) versus the IFCR-F group (3 ± 1 kg; 4 ± 1 cm). Similar reductions (P < 0.0001) in fat mass were demonstrated in the IFCR-L (3 ± 1 kg) and IFCR-F group (2 ± 1 kg). Reductions in total and LDL cholesterol levels were greater (P = 0.04) in the IFCR-L (19 ± 10%; 20 ± 9%, respectively) versus the IFCR-F group (8 ± 3%; 7 ± 4%, respectively). LDL peak particle size increased (P < 0.01) in the IFCR-L group only. The proportion of small LDL particles decreased (P < 0.01) in both groups. Adipokines, such as leptin, interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-alpha), and insulin-like growth factor-1 (IGF-1) decreased (P < 0.05), in the IFCR-L group only.

Conclusion
These findings suggest that IFCR with a liquid diet favorably modulates visceral fat and adipokines in a way that may confer protection against CHD.