bluuebunny/crossref_metadata_2025_split huggingface dataset:
Basic Residues in the Matrix Domain and Multimerization Target Murine Leukemia Virus Gag to the Virological Synapse
Authors: Li Fei , Jin Jing , Herrmann Christin , Mothes Walther 
Published: April 2013

ABSTRACT

Murine leukemia virus (MLV) can efficiently spread in tissue cultures by polarizing assembly to virological synapses. The viral envelope glycoprotein (Env) establishes cell-cell contacts and subsequently recruits Gag by a process that depends on its cytoplasmic tail. MLV Gag is recruited to virological synapses through the matrix domain (MA) (J. Jin, F. Li, and W. Mothes, J. Virol.
85:
7672–7682, 2011). However, how MA targets Gag to sites of cell-cell contact remains unknown. Here we report that basic residues within MA are critical for directing MLV Gag to virological synapses. Alternative membrane targeting domains (MTDs) containing multiple basic residues can efficiently substitute MA to direct polarized assembly. Similarly, mutations in the polybasic cluster of MA that disrupt Gag polarization can be rescued by N-terminal addition of MTDs containing basic residues. MTDs containing basic residues alone fail to be targeted to the virological synapse. Systematic deletion experiments reveal that domains within Gag known to mediate Gag multimerization are also required. Thus, our data predict the existence of a specific “acidic” interface at virological synapses that mediates the recruitment of MLV Gag via the basic cluster of MA and Gag multimerization.
New species and records of quill mites of the family Syringophilidae (Acari: Prostigmata) from the passerines (Aves: Passeriformes) from the Russian Far East
Authors: SKORACKI MACIEJ , MIRONOV SERGEY V. 
Published: April 2013

Two new species, Syringophilopisis pari sp. nov. from Poecile palustris Linnaeus (Paridae) and Torotrogla volgini sp. nov. from Emberiza elegans Temminck (Emberizidae) are described. Additionally, new host species are reported for three syringophilid species: Emberiza tristrami Swinhoe and E. rutila Pallas for Betasyringophiloidus schoeniclus (Skoracki); Sitta europaea Linnaeus (Sittidae) for Syringophilopsis sittae Skoracki et al., and Zosterops erythropleurus Swinhoe (Zos-teropidae) for Neoaulonastus zosterops Skoracki et al. All avian hosts were captured in the Primorsky Krai, Russia. The syringophilid fauna presently recorded from Russia is summarized. �� n-ȷ���5%'>20 in 2 species. The decrease in autosome number (14A) has been accompanied by 2 pairs of extremely large autosomes (Anoplocnemis binotata Distant and Cletus borealis Blöte) and the increase in autosome number (22A, 24A) has been accompanied by distinctly small autosomes (Petalocnemis obscura and Prionolomia sp.) in the complement. The behavior of chromosomes during meiosis is typical of Coreidae. Deviations wherever recorded are discussed. During diplotene, chiasmata are located terminally and there is a predominance of a single chiasma per bivalent. However, in Anoplocnemis binotata and Cletus borealis, one or both of the large bivalents show two terminal or subterminal chiasmata in diplotene. A regular arrangement of chromosomes is observed during both metaphase I and II: all the autosomes form a ring with microchromosomes lying inside and sex chromosomes lying outside the ring.
Impact of Low-Level Jets on the Nocturnal Urban Heat Island Intensity in Oklahoma City
Authors: Hu Xiao-Ming , Klein Petra M. , Xue Ming , Lundquist Julie K. , Zhang Fuqing , Qi Youcun 
Published: April 2013

AbstractPrevious analysis of Oklahoma City (OKC), Oklahoma, temperature data indicated that urban heat islands (UHIs) frequently formed at night and the observed UHI intensity was variable (1°–4°C). The current study focuses on identifying meteorological phenomena that contributed to the variability of nocturnal UHI intensity in OKC during July 2003. Two episodes, one with a strong UHI signature and one with a weak signature, were studied in detail using observations along with simulations with the Weather Research and Forecasting model. Mechanical mixing associated with low-level jets (LLJs) played a critical role in moderating the nocturnal UHI intensity. During nights with weak LLJs or in the absence of LLJs, vertical mixing weakened at night and strong temperature inversions developed in the rural surface layer as a result of radiative cooling. The shallow stable boundary layer (SBL < 200 m) observed under such conditions was strongly altered inside the city because rougher and warmer surface characteristics caused vertical mixing that eroded the near-surface inversion. Accordingly, temperatures measured within the urban canopy layer at night were consistently higher than at nearby rural sites of comparable height (by ~3°–4°C). During nights with strong LLJs, however, the jets facilitated enhanced turbulent mixing in the nocturnal boundary layer. As a consequence, atmospheric stability was much weaker and urban effects played a much less prominent role in altering the SBL structure; therefore, UHI intensities were smaller (<1°C) during strong LLJs. The finding that rural inversion strength can serve as an indicator for UHI intensity highlights that the structure of the nocturnal boundary layer is important for UHI assessments.
Decadal Prediction of the Sahelian Precipitation in CMIP5 Simulations
Authors: Gaetani Marco , Mohino Elsa 
Published: April 2013

Abstract
In this study the capability of eight state-of-the-art ocean–atmosphere coupled models in predicting the monsoonal precipitation in the Sahel on a decadal time scale is assessed. To estimate the importance of the initialization, the predictive skills of two different CMIP5 experiments are compared, a set of 10 decadal hindcasts initialized every 5 years in the period 1961–2009 and the historical simulations in the period 1961–2005. Results indicate that predictive skills are highly model dependent: the Fourth Generation Canadian Coupled Global Climate Model (CanCM4), Centre National de Recherches Météorologiques Coupled Global Climate Model, version 5 (CNRM-CM5), and Max Planck Institute Earth System Model, low resolution (MPI-ESM-LR) models show improved skill in the decadal hindcasts, while the Model for Interdisciplinary Research on Climate, version 5 (MIROC5) is skillful in both the decadal and historical experiments. The Beijing Climate Center, Climate System Model, version 1.1 (BCC-CSM1.1), Hadley Centre Coupled Model, version 3 (HadCM3), L'Institut Pierre-Simon Laplace Coupled Model, version 5, coupled with NEMO, low resolution (IPSL-CM5A-LR), and Meteorological Research Institute Coupled Atmosphere–Ocean General Circulation Model, version 3 (MRI-CGCM3) models show insignificant or no skill in predicting the Sahelian precipitation. Skillful predictions are produced by models properly describing the SST multidecadal variability and the initialization appears to play an important role in this respect.
The Surface Climate Response to 11-Yr Solar Forcing during Northern Winter: Observational Analyses and Comparisons with GCM Simulations
Authors: Hood Lon , Schimanke Semjon , Spangehl Thomas , Bal Sourabh , Cubasch Ulrich 
Published: April 2013

Abstract
The surface climate response to 11-yr solar forcing during northern winter is first reestimated by applying a multiple linear regression (MLR) statistical model to Hadley Centre sea level pressure (SLP) and sea surface temperature (SST) data over the 1880–2009 period. In addition to a significant positive SLP response in the North Pacific found in previous studies, a positive SST response is obtained across the midlatitude North Pacific. Negative but insignificant SLP responses are obtained in the Arctic. The derived SLP response at zero lag therefore resembles a positive phase of the Arctic Oscillation (AO). Evaluation of the SLP and SST responses as a function of phase lag indicates that the response evolves from a negative AO-like mode a few years before solar maximum to a positive AO-like mode at and following solar maximum. For comparison, a similar MLR analysis is applied to model SLP and SST data from a series of simulations using an atmosphere–ocean general circulation model with a well-resolved stratosphere. The simulations differed only in the assumed solar cycle variation of stratospheric ozone. It is found that the simulation that assumed an ozone variation estimated from satellite data produces solar SLP and SST responses that are most consistent with the observational results, especially during a selected centennial period. In particular, a positive SLP response anomaly is obtained in the northeastern Pacific and a corresponding positive SST response anomaly extends across the midlatitude North Pacific. The model response versus phase lag also evolves from a mainly negative AO-like response before solar maximum to a mainly positive AO response at and following solar maximum.
On the Longwave Climate Feedbacks
Authors: Huang Yi 
Published: April 2013

Abstract
This paper mainly addresses two issues that concern the longwave climate feedbacks. First, it is recognized that the radiative forcing of greenhouse gases, as measured by their impact on the outgoing longwave radiation (OLR), may vary across different climate models even when the concentrations of these gases are identically prescribed. This forcing variation contributes to the discrepancy in these models' projections of surface warming. A method is proposed to account for this effect in diagnosing the sensitivity and feedbacks in the models. Second, it is shown that the stratosphere is an important factor that affects the OLR in transient climate change. Stratospheric water vapor and temperature changes may both act as a positive feedback mechanism during global warming and cannot be fully accounted as a “stratospheric adjustment” of radiative forcing. Neglecting these two issues may cause a bias in the longwave cloud feedback diagnosed as a residual term in the decomposition of OLR variations. There is no consensus among the climate models on the sign of the longwave cloud feedback after accounting for both issues.
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Authors: Zhang Lifang , Zhang Juan , Yang Gang , Wu Di , Jiang Lina , Wen Zhining , Li Menglong 
Published: April 2013

Abstract

Background
Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food and Drug Administration (FDA) elucidated that the lists of DEGs generated by intra- and inter-platform comparisons can reach a high level of concordance, which mainly depended on the statistical criteria used for ranking and selecting DEGs. Generally, it will produce reproducible lists of DEGs when combining fold change ranking with a non-stringent p-value cutoff. For further interpretation of the gene expression data, statistical methods of gene enrichment analysis provide powerful tools for associating the DEGs with prior biological knowledge, e.g. Gene Ontology (GO) terms and pathways, and are widely used in genome-wide research. Although the DEG lists generated from the same compared conditions proved to be reliable, the reproducible enrichment results are still crucial to the discovery of the underlying molecular mechanism differentiating the two conditions. Therefore, it is important to know whether the enrichment results are still reproducible, when using the lists of DEGs generated by different statistic criteria from inter-laboratory and cross-platform comparisons. In our study, we used the MAQC data sets for systematically accessing the intra- and inter-platform concordance of GO terms enriched by Gene Set Enrichment Analysis (GSEA) and LRpath.

Results
In intra-platform comparisons, the overlapped percentage of enriched GO terms was as high as ~80% when the inputted lists of DEGs were generated by fold change ranking and Significance Analysis of Microarrays (SAM), whereas the percentages decreased about 20% when generating the lists of DEGs by using fold change ranking and t-test, or by using SAM and t-test. Similar results were found in inter-platform comparisons.

Conclusions
Our results demonstrated that the lists of DEGs in a high level of concordance can ensure the high concordance of enrichment results. Importantly, based on the lists of DEGs generated by a straightforward method of combining fold change ranking with a non-stringent p-value cutoff, enrichment analysis will produce reproducible enriched GO terms for the biological interpretation.
Effect of interleukin-6 polymorphism on risk of preterm birth within population strata: a meta-analysis
Authors: Wu Wilfred , Clark Erin A S , Stoddard Gregory J , Watkins W Scott , Esplin M Sean , Manuck Tracy A , Xing Jinchuan , Varner Michael W , Jorde Lynn B 
Published: April 2013

Abstract

Background
Because of the role of inflammation in preterm birth (PTB), polymorphisms in and near the interleukin-6 gene (IL6) have been association study targets. Several previous studies have assessed the association between PTB and a single nucleotide polymorphism (SNP), rs1800795, located in the IL6 gene promoter region. Their results have been inconsistent and SNP frequencies have varied strikingly among different populations. We therefore conducted a meta-analysis with subgroup analysis by population strata to: (1) reduce the confounding effect of population structure, (2) increase sample size and statistical power, and (3) elucidate the association between rs1800975 and PTB.

Results
We reviewed all published papers for PTB phenotype and SNP rs1800795 genotype. Maternal genotype and fetal genotype were analyzed separately and the analyses were stratified by population. The PTB phenotype was defined as gestational age (GA) < 37 weeks, but results from earlier GA were selected when available. All studies were compared by genotype (CC versus CG+GG), based on functional studies.
For the maternal genotype analysis, 1,165 PTBs and 3,830 term controls were evaluated. Populations were stratified into women of European descent (for whom the most data were available) and women of heterogeneous origin or admixed populations. All ancestry was self-reported. Women of European descent had a summary odds ratio (OR) of 0.68, (95% confidence interval (CI) 0.51 – 0.91), indicating that the CC genotype is protective against PTB. The result for non-European women was not statistically significant (OR 1.01, 95% CI 0.59 - 1.75). For the fetal genotype analysis, four studies were included; there was no significant association with PTB (OR 0.98, 95% CI 0.72 - 1.33). Sensitivity analysis showed that preterm premature rupture of membrane (PPROM) may be a confounding factor contributing to phenotype heterogeneity.

Conclusions

IL6 SNP rs1800795 genotype CC is protective against PTB in women of European descent. It is not significant in other heterogeneous or admixed populations, or in fetal genotype analysis.
Population structure is an important confounding factor that should be controlled for in studies of PTB.
VEGF is an important mediator of tumor angiogenesis in malignant lesions in a genetically engineered mouse model of lung adenocarcinoma
Authors: Majeti Bharat K , Lee Joseph H , Simmons Brett H , Shojaei Farbod 
Published: April 2013

Abstract

Background
VEGF is one of the key drivers of physiological or pathological angiogenesis hence several VEGF inhibitors are in different stages of clinical development. To further dissect the role of VEGF in different stages of tumor progression in lung tumors, we utilized KrasG12D-LSL GEMMs (genetically engineered mouse models).

Methods
Intranasal delivery of adenoviruses expressing cre recombinase in KrasG12D-LSL mice results in the expression of mutant Kras that leads to development of tumor lesions ranging from adenomatous hyperplasia to large adenoma and adenocarcinoma over time in lung. In the current study, we treated KrasG12D-LSL mice at 14 weeks post inhalation with three different angiogenic inhibitors including axitinib and PF-00337210 both of which are selective inhibitors of VEGFR and sunitinib which targets VEGFR, C-SF1-R, PDGFR and KIT.

Results
Pathology findings showed no significant difference in percentage of adenomatous hyperplastic lesions between the vehicle vs. any of the treatments suggesting that angiogenesis may not play a major role at early stages of tumorigenesis. However, each inhibitor suppressed percentage of benign adenoma lesions and almost fully inhibited growth of adenocarcinoma lesions in the recipients which was consistent with a reduction in tumor vasculature. Treatment with sunitinib which is a multi-targeted RTKI did not provide any advantage compared to selective VEGFR inhibitor further emphasizing role of VEGF in tumor angiogenesis in this model.

Conclusion
Overall, our studies indicate significance of VEGF and angiogenesis in a spontaneous model of lung tumorigenesis and provide a proof of mechanism for anti-cancer activity of VEGF inhibitors in this model.
A case of synchronous bilateral lung cancers: EML4-ALK positive adenocarcinoma in the right lung and adenocarcinoma in situ (the former bronchioloalveolar carcinoma) in the left lung
Authors: Matsuda Ikuo , Takeuchi Kengo , Mizuguchi Shinjiro , Kaji Masahide , Ueda Kayo , Teramura Kazuhiro , Hirota Seiichi 
Published: April 2013

Abstract

Background
Recently it has been revealed that lung adenocarcinomas with distinct gene mutations or fusions are associated with particular histopathological entities. For example, epidermal growth factor receptor (EGFR) gene mutations are often associated with well differentiated adenocarcinoma of the lung with bronchioloalveolar pattern. On the other hand, echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusion gene in a subset of lung adenocarcinoma is related to mucinous cribriform histology.

Case presentation
Reported herein is a case of synchronous EML4-ALK positive lung adenocarcinoma and adenocarcinoma in situ in the bilateral lungs of a 55-year-old Japanese woman. The woman had EML4-ALK positive lung adenocarcinoma in the right lower lung while adenocarcinoma in situ in the left upper lung, which was EML4-ALK negative.

Conclusion
To our knowledge, this is the first report of synchronous, bilateral lung adenocarcinomas composed of EML4-ALK positive and negative ones.
Sodium-Calcium Exchangers in Rat Trigeminal Ganglion Neurons
Authors: Kuroda Hidetaka , Sobhan Ubaidus , Sato Masaki , Tsumura Maki , Ichinohe Tatsuya , Tazaki Masakazu , Shibukawa Yoshiyuki 
Published: April 2013

Background Noxious stimulation and nerve injury induce an increase in intracellular Ca2+ concentration ([Ca2+]i) via various receptors or ionic channels. While an increase in [Ca2+]i excites neurons, [Ca2+]i overload elicits cytotoxicity, resulting in cell death. Intracellular Ca2+ is essential for many signal transduction mechanisms, and its level is precisely regulated by the Ca2+ extrusion system in the plasma membrane, which includes the Na+-Ca2+ exchanger (NCX). It has been demonstrated that Ca2+-ATPase is the primary mechanism for removing [Ca2+]i following excitatory activity in trigeminal ganglion (TG) neurons; however, the role of NCXs in this process has yet to be clarified. The goal of this study was to examine the expression/localization of NCXs in TG neurons and to evaluate their functional properties. Results NCX isoforms (NCX1, NCX2, and NCX3) were expressed in primary cultured rat TG neurons. All the NCX isoforms were also expressed in A-, peptidergic C-, and non-peptidergic C-neurons, and located not only in the somata, dendrites, axons and perinuclear region, but also in axons innervating the dental pulp. Reverse NCX activity was clearly observed in TG neurons. The inactivation kinetics of voltage-dependent Na+ channels were prolonged by NCX inhibitors when [Ca2+]i in TG neurons was elevated beyond physiological levels. Conclusions Our results suggest that NCXs in TG neurons play an important role in regulating Ca2+-homeostasis and somatosensory information processing by functionally coupling with voltage-dependent Na+ channels.
Silence between patients and doctors: the issue of self-determination and amniocentesis in Japan
Authors: Kato Masae 
Published: April 2013

Abstract
Japan is among the few countries that have passed laws concerning eugenics. Consequently, the practice of selective abortion (abortion of an abnormal foetus) has been publicly debated for the past 35 years. Nevertheless, data show that knowledge in Japan about prenatal diagnosis is anything but common. In my fieldwork (April- June 2006) only 38% of interviewees (13/34) knew or had heard of 'amniocentesis' and 6% knew nothing about it at all. There are many explanations for why people are unaware of prenatal diagnosis. The most crucial factor is that medical doctors do not talk to their patients about it. My interviews with 11 medical doctors revealed that they do not talk about it because they want to respect the principle of patient selfdetermination. In this paper I aim first to introduce and analyse, in the context of Japanese eugenic history and the contemporary notion of the patient-doctor relationship, medical doctors' explanations for not talking to their patients about amniocentesis. Second, I address whether the principle of 'non-intervention' equates to 'self-determination'. Lastly, I suggest possible improvements to the practice of 'self-determination' in Japan.
The application of PET-CT to post-mastectomy regional radiation therapy using a deformable image registration
Authors: Lee Yu Sun , Kim Kyoung Ju , Ahn Seung Do , Choi Eun Kyung , Kim Jong Hoon , Lee Sang-wook , Song Si Yeol , Yoon Sang Min , Kim Young Seok , Park Jin-hong , Cho Byung Chul , Kim Su Ssan 
Published: April 2013

Abstract

Background
To evaluate the utility of the preoperative PET-CT using deformable image registration (DIR) in the treatment of patients with locally advanced breast cancer and to find appropriate radiotherapy technique for further adequate treatment of axillary nodal area.

Methods
Sixty-five breast cancer patients who had level II, III axillary or supraclavicular lymph node metastasis on 18F-FDG PET-CT and received postoperative radiotherapy after modified radical mastectomy were enrolled. One radiation oncologist contoured normal organs (axillary vessels, clavicular head, coracoids process and humeral head) and involved lymph nodes on PET-CT and simulation CT slices. After contouring, deformable image registration of PET-CT on simulation CT was carried out. To evaluate the performance of the DIR, Dice similarity coefficient (DSC) and Center of mass (COM) were used. We created two plans, one was the historically designed three field plan and the other was the modified plan based on the location of axillary lymph node, and we compared the doses that irradiated the axillary lymph nodes.

Results
The DSCs for axillary artery, axillary vein, clavicular head, coracoids process and humeral head were 0.43 ± 0.15, 0.39 ± 0.20, 0.85 ± 0.10, 0.72 ± 0.20 and 0.77 ± 0.20, respectively. The distances between the COMs of axillary artery, axillary vein, clavicular head, coracoids process and humeral head in simulation CT and from PET-CT were 13.0 ±7.1, 20.2 ± 11.2, 4.4 ± 6.3, 3.7 ± 6.7, and 9.5 ± 25.0 mm, respectively. In the historically designed plan, only 57.7% of level II lymph nodes received more than 95% of prescribed dose and the coverage was improved to 70.0% with the modified plan (p < 0.01). For level III lymph nodes, the volumes received more than 95% of prescribed dose were similar in both plans (96.8 % vs 97.9%, p = 0.35).

Conclusion
Deformable image registration of PET-CT on simulation CT was helpful in the identification of the location of the preoperatively involved axillary lymph node. Historically designed three-field plan was not adequate to treat the axillary level II lymph node area. Novel treatment technique based on the location of axillary lymph node from PET-CT using DIR can result in more adequate coverage of nodal area.